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Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution

Source organism: Homo sapiens
Biochemical function: protein binding
Biological process: mRNA splicing, via spliceosome
Cellular component: nucleoplasm

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EC 2.3.2.27: RING-type E3 ubiquitin transferase

Reaction catalysed:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Systematic name:
[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein]-L-lysine ubiquitin transferase (isopeptide bond-forming; RING-type)
Alternative Name(s):
  • RING E3 ligase
  • Ubiquitin transferase RING E3

EC 5.2.1.8: Peptidylprolyl isomerase

Reaction catalysed:
Peptidylproline (omega=180) = peptidylproline (omega=0)
Systematic name:
Peptidylproline cis-trans-isomerase
Alternative Name(s):
  • Cyclophilin
  • PPIase
  • Peptide bond isomerase
  • Peptidyl-prolyl cis-trans isomerase
  • Peptidylprolyl cis-trans isomerase
  • Rotamase

EC 3.6.4.13: RNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (RNA helix unwinding)
Alternative Name(s):
  • CSFV NS3 helicase
  • DBP2
  • DDX17
  • DDX25
  • DDX3
  • DDX3X
  • DDX3Y
  • DDX4
  • DDX5
  • DEAD-box RNA helicase
  • DEAD-box protein DED1
  • DEAH-box RNA helicase
  • DEAH-box protein 2
  • DED1
  • DbpA
  • Dex(H/D) RNA helicase
  • EIF4A helicase
  • EhDEAD1
  • EhDEAD1 RNA helicase
  • GRTH/DDX25
  • KOKV helicase
  • Mtr4p
  • NPH-II
  • Nonstructural protein 3 helicase
  • RHA
  • RNA helicase A
  • RNA helicase DDX3
  • RNA helicase Hera
  • RNA-dependent ATPase
  • TGBp1 NTPase/helicase domain
  • VRH1

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00400
Domain description: WD domain, G-beta repeat
Occurring in:
  1. U5 small nuclear ribonucleoprotein 40 kDa protein
  2. Pleiotropic regulator 1
  3. Pre-mRNA-processing factor 17
  4. Pre-mRNA-processing factor 19
The deposited structure of PDB entry 6id1 contains 7 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in U5 small nuclear ribonucleoprotein 40 kDa protein. Showing 7 copies in chain D [auth E].
The deposited structure of PDB entry 6id1 contains 5 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in Pleiotropic regulator 1. Showing 5 copies in chain N [auth T].
The deposited structure of PDB entry 6id1 contains 5 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in Pre-mRNA-processing factor 17. Showing 5 copies in chain O [auth W] (this domain is out of the observed residue ranges!).
The deposited structure of PDB entry 6id1 contains 20 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in Pre-mRNA-processing factor 19. Showing 5 copies in chain Z [auth q] (this domain is out of the observed residue ranges!).

PF01423
Domain description: LSM domain
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D3
  2. Small nuclear ribonucleoprotein-associated proteins B and B'
  3. Small nuclear ribonucleoprotein Sm D1
  4. Small nuclear ribonucleoprotein Sm D2
  5. Small nuclear ribonucleoprotein E
  6. Small nuclear ribonucleoprotein F
  7. Small nuclear ribonucleoprotein G
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF01423 (LSM domain) in Small nuclear ribonucleoprotein Sm D3. Showing 1 copy in chain S [auth a].
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF01423 (LSM domain) in Small nuclear ribonucleoprotein-associated proteins B and B'. Showing 1 copy in chain T [auth b].
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF01423 (LSM domain) in Small nuclear ribonucleoprotein Sm D1. Showing 1 copy in chain JA [auth j].
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF01423 (LSM domain) in Small nuclear ribonucleoprotein Sm D2. Showing 1 copy in chain V [auth d].
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF01423 (LSM domain) in Small nuclear ribonucleoprotein F. Showing 1 copy in chain LA [auth m].
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF01423 (LSM domain) in Small nuclear ribonucleoprotein E. Showing 1 copy in chain MA [auth l].
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF01423 (LSM domain) in Small nuclear ribonucleoprotein G. Showing 1 copy in chain Y [auth g].

PF08606
Domain description: Prp19/Pso4-like
Occurring in:
  1. Pre-mRNA-processing factor 19
The deposited structure of PDB entry 6id1 contains 4 copies of Pfam domain PF08606 (Prp19/Pso4-like) in Pre-mRNA-processing factor 19. Showing 1 copy in chain Z [auth q].

PF04564
Domain description: U-box domain
Occurring in:
  1. Pre-mRNA-processing factor 19
The deposited structure of PDB entry 6id1 contains 4 copies of Pfam domain PF04564 (U-box domain) in Pre-mRNA-processing factor 19. Showing 1 copy in chain Z [auth q].

PF00076
Domain description: RNA recognition motif
Occurring in:
  1. Pre-mRNA-splicing factor RBM22
  2. U2 small nuclear ribonucleoprotein B''
  3. Peptidyl-prolyl cis-trans isomerase E
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00076 (RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)) in Pre-mRNA-splicing factor RBM22. Showing 1 copy in chain J [auth O].
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00076 (RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)) in Peptidyl-prolyl cis-trans isomerase E. Showing 1 copy in chain GA [auth y].
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF00076 (RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)) in U2 small nuclear ribonucleoprotein B''. Showing 2 copies in chain PA [auth p] (some of the copies are out of the observed residue ranges!).

PF00160
Domain description: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase-like 1
  2. Peptidyl-prolyl cis-trans isomerase E
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00160 (Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD) in Peptidyl-prolyl cis-trans isomerase-like 1. Showing 1 copy in chain M [auth S].
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00160 (Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD) in Peptidyl-prolyl cis-trans isomerase E. Showing 1 copy in chain GA [auth y] (this domain is out of the observed residue ranges!).

PF13921
Domain description: Myb-like DNA-binding domain
Occurring in:
  1. Cell division cycle 5-like protein
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF13921 (Myb-like DNA-binding domain) in Cell division cycle 5-like protein. Showing 2 copies in chain G [auth L].

PF02184
Domain description: HAT (Half-A-TPR) repeat
Occurring in:
  1. Crooked neck-like protein 1
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF02184 (HAT (Half-A-TPR) repeat) in Crooked neck-like protein 1. Showing 2 copies in chain F [auth J].

PF13181
Domain description: Tetratricopeptide repeat
Occurring in:
  1. Pre-mRNA-splicing factor SYF1
The deposited structure of PDB entry 6id1 contains 2 copies of Pfam domain PF13181 (Tetratricopeptide repeat) in Pre-mRNA-splicing factor SYF1. Showing 2 copies in chain EA [auth I].

PF14580
Domain description: Leucine-rich repeat
Occurring in:
  1. U2 small nuclear ribonucleoprotein A'
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF14580 (Leucine-rich repeat) in U2 small nuclear ribonucleoprotein A'. Showing 1 copy in chain OA [auth o].

PF07717
Domain description: Oligonucleotide/oligosaccharide-binding (OB)-fold
Occurring in:
  1. ATP-dependent RNA helicase DHX15
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF07717 (Oligonucleotide/oligosaccharide-binding (OB)-fold) in ATP-dependent RNA helicase DHX15. Showing 1 copy in chain QA [auth V].

PF21010
Domain description: Helicase associated domain (HA2), ratchet-like
Occurring in:
  1. ATP-dependent RNA helicase DHX15

PF04408
Domain description: Helicase associated domain (HA2), winged-helix
Occurring in:
  1. ATP-dependent RNA helicase DHX15
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF04408 (Helicase associated domain (HA2)) in ATP-dependent RNA helicase DHX15. Showing 1 copy in chain QA [auth V].

PF00271
Domain description: Helicase conserved C-terminal domain
Occurring in:
  1. ATP-dependent RNA helicase DHX15
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00271 (Helicase conserved C-terminal domain) in ATP-dependent RNA helicase DHX15. Showing 1 copy in chain QA [auth V].

PF00270
Domain description: DEAD/DEAH box helicase
Occurring in:
  1. ATP-dependent RNA helicase DHX15
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00270 (DEAD/DEAH box helicase) in ATP-dependent RNA helicase DHX15. Showing 1 copy in chain QA [auth V].

PF04676
Domain description: Protein similar to CwfJ C-terminus 2
Occurring in:
  1. CWF19-like protein 2
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF04676 (Protein similar to CwfJ C-terminus 2) in CWF19-like protein 2. Showing 1 copy in chain R [auth U].

PF04677
Domain description: Protein similar to CwfJ C-terminus 1
Occurring in:
  1. CWF19-like protein 2
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF04677 (Protein similar to CwfJ C-terminus 1) in CWF19-like protein 2. Showing 1 copy in chain R [auth U].

PF02731
Domain description: SKIP/SNW domain
Occurring in:
  1. SNW domain-containing protein 1
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF02731 (SKIP/SNW domain) in SNW domain-containing protein 1. Showing 1 copy in chain L [auth R].

PF13087
Domain description: AAA domain
Occurring in:
  1. RNA helicase aquarius
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF13087 (AAA domain) in RNA helicase aquarius. Showing 1 copy in chain FA [auth Q].

PF13086
Domain description: AAA domain
Occurring in:
  1. RNA helicase aquarius
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF13086 (AAA domain) in RNA helicase aquarius. Showing 1 copy in chain FA [auth Q].

PF21144
Domain description: Intron-binding protein aquarius insert domain
Occurring in:
  1. RNA helicase aquarius

PF21143
Domain description: Intron-binding protein aquarius, beta-barrel
Occurring in:
  1. RNA helicase aquarius

PF16399
Domain description: Intron-binding protein aquarius N-terminal
Occurring in:
  1. RNA helicase aquarius
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF16399 (Intron-binding protein aquarius N-terminus) in RNA helicase aquarius. Showing 1 copy in chain FA [auth Q].

PF04889
Domain description: Cwf15/Cwc15 cell cycle control protein
Occurring in:
  1. Spliceosome-associated protein CWC15 homolog
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF04889 (Cwf15/Cwc15 cell cycle control protein) in Spliceosome-associated protein CWC15 homolog. Showing 1 copy in chain K [auth P].

PF21369
Domain description: STL11, N-terminal
Occurring in:
  1. Pre-mRNA-splicing factor RBM22

PF01125
Domain description: Pre-mRNA-splicing factor BUD31
Occurring in:
  1. Protein BUD31 homolog
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF01125 (G10 protein) in Protein BUD31 homolog. Showing 1 copy in chain I [auth N].

PF08231
Domain description: SYF2 splicing factor
Occurring in:
  1. Pre-mRNA-splicing factor SYF2
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF08231 (SYF2 splicing factor) in Pre-mRNA-splicing factor SYF2. Showing 1 copy in chain H [auth M].

PF11831
Domain description: pre-mRNA splicing factor component
Occurring in:
  1. Cell division cycle 5-like protein
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF11831 (pre-mRNA splicing factor component) in Cell division cycle 5-like protein. Showing 1 copy in chain G [auth L].

PF05700
Domain description: Breast carcinoma amplified sequence 2 (BCAS2)
Occurring in:
  1. Pre-mRNA-splicing factor SPF27
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF05700 (Breast carcinoma amplified sequence 2 (BCAS2)) in Pre-mRNA-splicing factor SPF27. Showing 1 copy in chain DA [auth K].

PF00679
Domain description: Elongation factor G C-terminus
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00679 (Elongation factor G C-terminus) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain C.

PF03764
Domain description: Elongation factor G, domain IV
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF03764 (Elongation factor G, domain IV) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain C.

PF14492
Domain description: Elongation Factor G, domain III
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF14492 (Elongation Factor G, domain III) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain C.

PF03144
Domain description: Elongation factor Tu domain 2
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF03144 (Elongation factor Tu domain 2) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain C.

PF00009
Domain description: Elongation factor Tu GTP binding domain
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF00009 (Elongation factor Tu GTP binding domain) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain C.

PF16004
Domain description: 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF16004 (116 kDa U5 small nuclear ribonucleoprotein component N-terminus) in 116 kDa U5 small nuclear ribonucleoprotein component. Showing 1 copy in chain C.

PF08084
Domain description: PROCT (NUC072) domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF08084 (PROCT (NUC072) domain) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A (this domain is out of the observed residue ranges!).

PF01398
Domain description: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF01398 (JAB1/Mov34/MPN/PAD-1 ubiquitin protease) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A (this domain is out of the observed residue ranges!).

PF12134
Domain description: PRP8 domain IV core
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF12134 (PRP8 domain IV core) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A.

PF10596
Domain description: U6-snRNA interacting domain of PrP8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF10596 (U6-snRNA interacting domain of PrP8) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A.

PF10597
Domain description: U5-snRNA binding site 2 of PrP8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF10597 (U5-snRNA binding site 2 of PrP8) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A.

PF10598
Domain description: RNA recognition motif of the spliceosomal PrP8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF10598 (RNA recognition motif of the spliceosomal PrP8) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A.

PF08083
Domain description: PROCN (NUC071) domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF08083 (PROCN (NUC071) domain) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A.

PF08082
Domain description: PRO8NT (NUC069), PrP8 N-terminal domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
The deposited structure of PDB entry 6id1 contains 1 copy of Pfam domain PF08082 (PRO8NT (NUC069), PrP8 N-terminal domain) in Pre-mRNA-processing-splicing factor 8. Showing 1 copy in chain A.

Rfam RNA families (Rfam)
RF00020
Domain description: U5 spliceosomal RNA
Occurring in:
  1. U5snRNA
The deposited structure of PDB entry 6id1 contains 1 copy of Rfam domain RF00020 (U5 spliceosomal RNA) in U5snRNA. Showing 1 copy in chain B.

RF00026
Domain description: U6 spliceosomal RNA
Occurring in:
  1. U6snRNA
The deposited structure of PDB entry 6id1 contains 1 copy of Rfam domain RF00026 (U6 spliceosomal RNA) in U6snRNA. Showing 1 copy in chain E [auth F].

RF00004
Domain description: U2 spliceosomal RNA
Occurring in:
  1. U2snRNA
The deposited structure of PDB entry 6id1 contains 1 copy of Rfam domain RF00004 (U2 spliceosomal RNA) in U2snRNA. Showing 1 copy in chain Q [auth H].

InterPro InterPro annotations
IPR001680
Domain description: WD40 repeat
Occurring in:
  1. U5 small nuclear ribonucleoprotein 40 kDa protein
  2. Pleiotropic regulator 1
  3. Pre-mRNA-processing factor 17
  4. Pre-mRNA-processing factor 19
IPR001163
Domain description: Sm domain, eukaryotic/archaea-type
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D3
  2. Small nuclear ribonucleoprotein-associated proteins B and B'
  3. Small nuclear ribonucleoprotein Sm D1
  4. Small nuclear ribonucleoprotein Sm D2
  5. Small nuclear ribonucleoprotein E
  6. Small nuclear ribonucleoprotein F
  7. Small nuclear ribonucleoprotein G
IPR003107
Domain description: HAT (Half-A-TPR) repeat
Occurring in:
  1. Pre-mRNA-splicing factor SYF1
  2. Crooked neck-like protein 1
IPR020472
Domain description: G-protein beta WD-40 repeat
Occurring in:
  1. U5 small nuclear ribonucleoprotein 40 kDa protein
  2. Pleiotropic regulator 1
  3. Pre-mRNA-processing factor 19
IPR010920
Domain description: LSM domain superfamily
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D3
  2. Small nuclear ribonucleoprotein-associated proteins B and B'
  3. Small nuclear ribonucleoprotein Sm D1
  4. Small nuclear ribonucleoprotein Sm D2
  5. Small nuclear ribonucleoprotein E
  6. Small nuclear ribonucleoprotein F
  7. Small nuclear ribonucleoprotein G
IPR047575
Domain description: Sm domain
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D3
  2. Small nuclear ribonucleoprotein-associated proteins B and B'
  3. Small nuclear ribonucleoprotein Sm D1
  4. Small nuclear ribonucleoprotein Sm D2
  5. Small nuclear ribonucleoprotein E
  6. Small nuclear ribonucleoprotein F
  7. Small nuclear ribonucleoprotein G
IPR002130
Domain description: Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase-like 1
  2. Peptidyl-prolyl cis-trans isomerase E
IPR011990
Domain description: Tetratricopeptide-like helical domain superfamily
Occurring in:
  1. Pre-mRNA-splicing factor SYF1
  2. Crooked neck-like protein 1
IPR003613
Domain description: U-box domain
Occurring in:
  1. Pre-mRNA-processing factor 19
IPR000504
Domain description: RNA recognition motif domain
Occurring in:
  1. Pre-mRNA-splicing factor RBM22
  2. U2 small nuclear ribonucleoprotein B''
  3. Peptidyl-prolyl cis-trans isomerase E
IPR019775
Domain description: WD40 repeat, conserved site
Occurring in:
  1. U5 small nuclear ribonucleoprotein 40 kDa protein
  2. Pleiotropic regulator 1
  3. Pre-mRNA-processing factor 17
  4. Pre-mRNA-processing factor 19
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
  2. RNA helicase aquarius
  3. ATP-dependent RNA helicase DHX15
IPR036322
Domain description: WD40-repeat-containing domain superfamily
Occurring in:
  1. U5 small nuclear ribonucleoprotein 40 kDa protein
  2. Pleiotropic regulator 1
  3. Pre-mRNA-processing factor 17
  4. Pre-mRNA-processing factor 19
IPR015943
Domain description: WD40/YVTN repeat-like-containing domain superfamily
Occurring in:
  1. U5 small nuclear ribonucleoprotein 40 kDa protein
  2. Pleiotropic regulator 1
  3. Pre-mRNA-processing factor 17
  4. Pre-mRNA-processing factor 19
IPR000795
Domain description: Translational (tr)-type GTP-binding domain
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR001748
Domain description: Pre-mRNA-splicing factor BUD31
Occurring in:
  1. Protein BUD31 homolog
IPR001005
Domain description: SANT/Myb domain
Occurring in:
  1. Cell division cycle 5-like protein
IPR019734
Domain description: Tetratricopeptide repeat
Occurring in:
  1. Pre-mRNA-splicing factor SYF1
IPR013915
Domain description: Pre-mRNA-splicing factor 19
Occurring in:
  1. Pre-mRNA-processing factor 19
IPR013083
Domain description: Zinc finger, RING/FYVE/PHD-type
Occurring in:
  1. Pre-mRNA-processing factor 19
IPR038959
Domain description: Pre-mRNA-processing factor 19
Occurring in:
  1. Pre-mRNA-processing factor 19
IPR027078
Domain description: Small nuclear ribonucleoprotein E
Occurring in:
  1. Small nuclear ribonucleoprotein E
IPR027248
Domain description: Small nuclear ribonucleoprotein Sm D2
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D2
IPR027141
Domain description: Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D3
  2. Small nuclear ribonucleoprotein Sm D1
IPR029000
Domain description: Cyclophilin-like domain superfamily
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase-like 1
  2. Peptidyl-prolyl cis-trans isomerase E
IPR012677
Domain description: Nucleotide-binding alpha-beta plait domain superfamily
Occurring in:
  1. Pre-mRNA-splicing factor RBM22
  2. U2 small nuclear ribonucleoprotein B''
  3. Peptidyl-prolyl cis-trans isomerase E
IPR001650
Domain description: Helicase, C-terminal domain-like
Occurring in:
  1. ATP-dependent RNA helicase DHX15
IPR035979
Domain description: RNA-binding domain superfamily
Occurring in:
  1. Pre-mRNA-splicing factor RBM22
  2. U2 small nuclear ribonucleoprotein B''
  3. Peptidyl-prolyl cis-trans isomerase E
IPR034168
Domain description: Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase E
IPR034098
Domain description: Small nuclear ribonucleoprotein G
Occurring in:
  1. Small nuclear ribonucleoprotein G
IPR044641
Domain description: Sm-like protein Lsm7/SmG
Occurring in:
  1. Small nuclear ribonucleoprotein G
IPR034100
Domain description: Small nuclear ribonucleoprotein F
Occurring in:
  1. Small nuclear ribonucleoprotein F
IPR016487
Domain description: Sm-like protein Lsm6/SmF
Occurring in:
  1. Small nuclear ribonucleoprotein F
IPR034102
Domain description: Small nuclear ribonucleoprotein D1
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D1
IPR017131
Domain description: Small ribonucleoprotein associated, SmB/SmN
Occurring in:
  1. Small nuclear ribonucleoprotein-associated proteins B and B'
IPR034099
Domain description: Small nuclear ribonucleoprotein Sm D3
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D3
IPR007502
Domain description: Helicase-associated domain
Occurring in:
  1. ATP-dependent RNA helicase DHX15
IPR014001
Domain description: Helicase superfamily 1/2, ATP-binding domain
Occurring in:
  1. ATP-dependent RNA helicase DHX15
IPR036265
Domain description: HIT-like superfamily
Occurring in:
  1. CWF19-like protein 2
IPR020892
Domain description: Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase-like 1
  2. Peptidyl-prolyl cis-trans isomerase E
IPR000571
Domain description: Zinc finger, CCCH-type
Occurring in:
  1. Pre-mRNA-splicing factor RBM22
IPR018230
Domain description: BUD31/G10-related, conserved site
Occurring in:
  1. Protein BUD31 homolog
IPR013260
Domain description: mRNA splicing factor SYF2
Occurring in:
  1. Pre-mRNA-splicing factor SYF2
IPR017930
Domain description: Myb domain
Occurring in:
  1. Cell division cycle 5-like protein
IPR008409
Domain description: Pre-mRNA-splicing factor SPF27
Occurring in:
  1. Pre-mRNA-splicing factor SPF27
IPR045075
Domain description: Pre-mRNA-splicing factor Syf1-like
Occurring in:
  1. Pre-mRNA-splicing factor SYF1
  2. Crooked neck-like protein 1
IPR000640
Domain description: Elongation factor EFG, domain V-like
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR005517
Domain description: Translation elongation factor EFG/EF2, domain IV
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR035647
Domain description: EF-G domain III/V-like
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR000555
Domain description: JAB1/MPN/MOV34 metalloenzyme domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR021983
Domain description: PRP8 domain IV core
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR012337
Domain description: Ribonuclease H-like superfamily
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR016304
Domain description: Peptidyl-prolyl cis-trans isomerase E
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase E
IPR034562
Domain description: U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2
Occurring in:
  1. U2 small nuclear ribonucleoprotein B''
IPR034564
Domain description: U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1
Occurring in:
  1. U2 small nuclear ribonucleoprotein B''
IPR003603
Domain description: U2A'/phosphoprotein 32 family A, C-terminal
Occurring in:
  1. U2 small nuclear ribonucleoprotein A'
IPR001611
Domain description: Leucine-rich repeat
Occurring in:
  1. U2 small nuclear ribonucleoprotein A'
IPR044640
Domain description: U2 small nuclear ribonucleoprotein A'
Occurring in:
  1. U2 small nuclear ribonucleoprotein A'
IPR032675
Domain description: Leucine-rich repeat domain superfamily
Occurring in:
  1. U2 small nuclear ribonucleoprotein A'
IPR032847
Domain description: Pre-mRNA-processing factor 17
Occurring in:
  1. Pre-mRNA-processing factor 17
IPR011709
Domain description: DEAD-box helicase, OB fold
Occurring in:
  1. ATP-dependent RNA helicase DHX15
IPR002464
Domain description: DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site
Occurring in:
  1. ATP-dependent RNA helicase DHX15
IPR011545
Domain description: DEAD/DEAH box helicase domain
Occurring in:
  1. ATP-dependent RNA helicase DHX15
IPR044756
Domain description: DHX15, DEXH-box helicase domain
Occurring in:
  1. ATP-dependent RNA helicase DHX15
IPR006767
Domain description: Cwf19-like protein, C-terminal domain-2
Occurring in:
  1. CWF19-like protein 2
IPR006768
Domain description: Cwf19-like, C-terminal domain-1
Occurring in:
  1. CWF19-like protein 2
IPR040194
Domain description: Cwf19-like protein
Occurring in:
  1. CWF19-like protein 2
IPR045241
Domain description: WD repeat Prp46/PLRG1-like
Occurring in:
  1. Pleiotropic regulator 1
IPR044666
Domain description: Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase-like 1
IPR024936
Domain description: Cyclophilin-type peptidyl-prolyl cis-trans isomerase
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase-like 1
IPR004015
Domain description: SKI-interacting protein SKIP, SNW domain
Occurring in:
  1. SNW domain-containing protein 1
IPR017862
Domain description: SKI-interacting protein, SKIP
Occurring in:
  1. SNW domain-containing protein 1
IPR047187
Domain description: Upf1-like, C-terminal helicase domain
Occurring in:
  1. RNA helicase aquarius
IPR041679
Domain description: DNA2/NAM7 helicase-like, C-terminal
Occurring in:
  1. RNA helicase aquarius
IPR041677
Domain description: DNA2/NAM7 helicase, helicase domain
Occurring in:
  1. RNA helicase aquarius
IPR045055
Domain description: DNA2/NAM7-like helicase
Occurring in:
  1. RNA helicase aquarius
IPR032174
Domain description: RNA helicase aquarius, N-terminal domain
Occurring in:
  1. RNA helicase aquarius
IPR026300
Domain description: CWF11 family
Occurring in:
  1. RNA helicase aquarius
IPR006973
Domain description: Pre-mRNA-splicing factor Cwf15/Cwc15
Occurring in:
  1. Spliceosome-associated protein CWC15 homolog
IPR036855
Domain description: Zinc finger, CCCH-type superfamily
Occurring in:
  1. Pre-mRNA-splicing factor RBM22
IPR039171
Domain description: Pre-mRNA-splicing factor Cwc2/Slt11
Occurring in:
  1. Pre-mRNA-splicing factor RBM22
IPR021786
Domain description: Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal
Occurring in:
  1. Cell division cycle 5-like protein
IPR047240
Domain description: Pre-mRNA splicing factor component CDC5L/Cef1, second SANT/myb-like domain
Occurring in:
  1. Cell division cycle 5-like protein
IPR009057
Domain description: Homeobox-like domain superfamily
Occurring in:
  1. Cell division cycle 5-like protein
IPR047242
Domain description: Pre-mRNA splicing factor component CDC5L/Cef1
Occurring in:
  1. Cell division cycle 5-like protein
IPR035655
Domain description: 116kDa U5 small nuclear ribonucleoprotein component, C-terminal
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR014721
Domain description: Small ribosomal subunit protein uS5 domain 2-type fold, subgroup
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR020568
Domain description: Ribosomal protein uS5 domain 2-type superfamily
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR041095
Domain description: Elongation Factor G, domain II
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR004161
Domain description: Translation elongation factor EFTu-like, domain 2
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR009000
Domain description: Translation protein, beta-barrel domain superfamily
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR044121
Domain description: Snu114, GTP-binding domain
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR005225
Domain description: Small GTP-binding protein domain
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR031950
Domain description: 116kDa U5 small nuclear ribonucleoprotein component, N-terminal
Occurring in:
  1. 116 kDa U5 small nuclear ribonucleoprotein component
IPR012984
Domain description: PROCT domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR037518
Domain description: MPN domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR043173
Domain description: Prp8 RNase domain IV, fingers region
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR043172
Domain description: Prp8 RNase domain IV, palm region
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR019580
Domain description: Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR019581
Domain description: Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR042516
Domain description: Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR019582
Domain description: RNA recognition motif, spliceosomal PrP8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR012592
Domain description: PROCN domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR012591
Domain description: PRO8NT domain
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8
IPR027652
Domain description: Pre-mRNA-processing-splicing factor 8
Occurring in:
  1. Pre-mRNA-processing-splicing factor 8

Structure domains

CATH CATH domains
2.30.30.100
Class: Mainly Beta
Architecture: Roll
Topology: SH3 type barrels.
Homology: SH3 type barrels.
Occurring in:
  1. Small nuclear ribonucleoprotein Sm D3
  2. Small nuclear ribonucleoprotein Sm D1
  3. Small nuclear ribonucleoprotein Sm D2
  4. Small nuclear ribonucleoprotein E
  5. Small nuclear ribonucleoprotein F
  6. Small nuclear ribonucleoprotein G
The deposited structure of PDB entry 6id1 contains 2 copies of CATH domain 2.30.30.100 (SH3 type barrels.) in Small nuclear ribonucleoprotein Sm D3. Showing 1 copy in chain S [auth a].
The deposited structure of PDB entry 6id1 contains 2 copies of CATH domain 2.30.30.100 (SH3 type barrels.) in Small nuclear ribonucleoprotein Sm D1. Showing 1 copy in chain U [auth c].
The deposited structure of PDB entry 6id1 contains 2 copies of CATH domain 2.30.30.100 (SH3 type barrels.) in Small nuclear ribonucleoprotein Sm D2. Showing 1 copy in chain V [auth d].
The deposited structure of PDB entry 6id1 contains 2 copies of CATH domain 2.30.30.100 (SH3 type barrels.) in Small nuclear ribonucleoprotein F. Showing 1 copy in chain W [auth f].
The deposited structure of PDB entry 6id1 contains 2 copies of CATH domain 2.30.30.100 (SH3 type barrels.) in Small nuclear ribonucleoprotein E. Showing 1 copy in chain X [auth e].
The deposited structure of PDB entry 6id1 contains 2 copies of CATH domain 2.30.30.100 (SH3 type barrels.) in Small nuclear ribonucleoprotein G. Showing 1 copy in chain Y [auth g].
3.30.70.330
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Alpha-Beta Plaits
Occurring in:
  1. U2 small nuclear ribonucleoprotein B''
  2. Peptidyl-prolyl cis-trans isomerase E
The deposited structure of PDB entry 6id1 contains 1 copy of CATH domain 3.30.70.330 (Alpha-Beta Plaits) in Peptidyl-prolyl cis-trans isomerase E. Showing 1 copy in chain GA [auth y].
The deposited structure of PDB entry 6id1 contains 1 copy of CATH domain 3.30.70.330 (Alpha-Beta Plaits) in U2 small nuclear ribonucleoprotein B''. Showing 1 copy in chain PA [auth p].
3.80.10.10
Class: Alpha Beta
Architecture: Alpha-Beta Horseshoe
Topology: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homology: Ribonuclease Inhibitor
Occurring in:
  1. U2 small nuclear ribonucleoprotein A'
The deposited structure of PDB entry 6id1 contains 1 copy of CATH domain 3.80.10.10 (Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)) in U2 small nuclear ribonucleoprotein A'. Showing 1 copy in chain OA [auth o].
2.40.100.10
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Cyclophilin
Homology: Cyclophilin-like
Occurring in:
  1. Peptidyl-prolyl cis-trans isomerase-like 1
The deposited structure of PDB entry 6id1 contains 1 copy of CATH domain 2.40.100.10 (Cyclophilin) in Peptidyl-prolyl cis-trans isomerase-like 1. Showing 1 copy in chain M [auth S].
2.130.10.10
Class: Mainly Beta
Architecture: 7 Propeller
Topology: Methylamine Dehydrogenase; Chain H
Homology: YVTN repeat-like/Quinoprotein amine dehydrogenase
Occurring in:
  1. U5 small nuclear ribonucleoprotein 40 kDa protein
The deposited structure of PDB entry 6id1 contains 1 copy of CATH domain 2.130.10.10 (Methylamine Dehydrogenase; Chain H) in U5 small nuclear ribonucleoprotein 40 kDa protein. Showing 1 copy in chain D [auth E].

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