› › Function and Biology

Body region of the U4/U6.U5 tri-snRNP

Source organism: Saccharomyces cerevisiae
Biochemical function: protein binding
Biological process: RNA splicing
Cellular component: U4/U6 x U5 tri-snRNP complex

Quick links

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

Sequence families

Pfam Protein families (Pfam)
PF00400
Domain description: WD domain, G-beta repeat
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP4
The deposited structure of PDB entry 5gap contains 4 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in U4/U6 small nuclear ribonucleoprotein PRP4. Showing 4 copies in chain F [auth H].

PF02889
Domain description: Sec63 Brl domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
The deposited structure of PDB entry 5gap contains 2 copies of Pfam domain PF02889 (Sec63 Brl domain) in Pre-mRNA-splicing helicase BRR2. Showing 2 copies in chain L [auth B] (this domain is out of the observed residue ranges!).

PF00270
Domain description: DEAD/DEAH box helicase
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
The deposited structure of PDB entry 5gap contains 2 copies of Pfam domain PF00270 (DEAD/DEAH box helicase) in Pre-mRNA-splicing helicase BRR2. Showing 2 copies in chain L [auth B] (this domain is out of the observed residue ranges!).

PF01248
Domain description: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Occurring in:
  1. 13 kDa ribonucleoprotein-associated protein
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF01248 (Ribosomal protein L7Ae/L30e/S12e/Gadd45 family) in 13 kDa ribonucleoprotein-associated protein. Showing 1 copy in chain K.

PF06424
Domain description: PRP1 splicing factor, N-terminal
Occurring in:
  1. Pre-mRNA-splicing factor 6
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF06424 (PRP1 splicing factor, N-terminal) in Pre-mRNA-splicing factor 6. Showing 1 copy in chain G [auth J] (this domain is out of the observed residue ranges!).

PF06544
Domain description: Small nuclear ribonucleoprotein Prp3, C-terminal domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP3
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF06544 (Protein of unknown function (DUF1115)) in U4/U6 small nuclear ribonucleoprotein PRP3. Showing 1 copy in chain J [auth G].

PF08572
Domain description: pre-mRNA processing factor 3 domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP3
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF08572 (pre-mRNA processing factor 3 (PRP3)) in U4/U6 small nuclear ribonucleoprotein PRP3. Showing 1 copy in chain J [auth G].

PF09785
Domain description: Prp31 C terminal domain
Occurring in:
  1. Pre-mRNA-processing factor 31
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF09785 (Prp31 C terminal domain) in Pre-mRNA-processing factor 31. Showing 1 copy in chain I [auth F].

PF01798
Domain description: snoRNA binding domain, fibrillarin
Occurring in:
  1. Pre-mRNA-processing factor 31
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF01798 (snoRNA binding domain, fibrillarin) in Pre-mRNA-processing factor 31. Showing 1 copy in chain I [auth F].

PF02966
Domain description: Mitosis protein DIM1
Occurring in:
  1. Spliceosomal protein DIB1
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF02966 (Mitosis protein DIM1) in Spliceosomal protein DIB1. Showing 1 copy in chain H [auth D].

PF00271
Domain description: Helicase conserved C-terminal domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF00271 (Helicase conserved C-terminal domain) in Pre-mRNA-splicing helicase BRR2. Showing 1 copy in chain L [auth B] (this domain is out of the observed residue ranges!).

PF18149
Domain description: N-terminal helicase PWI domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF18149 (N-terminal helicase PWI domain) in Pre-mRNA-splicing helicase BRR2. Showing 1 copy in chain L [auth B].

PF21188
Domain description: Pre-mRNA-splicing helicase BRR2 plug domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2

PF08084
Domain description: PROCT (NUC072) domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF08084 (PROCT (NUC072) domain) in Pre-mRNA-splicing factor 8. Showing 1 copy in chain E [auth A] (this domain is out of the observed residue ranges!).

PF12134
Domain description: PRP8 domain IV core
Occurring in:
  1. Pre-mRNA-splicing factor 8
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF12134 (PRP8 domain IV core) in Pre-mRNA-splicing factor 8. Showing 1 copy in chain E [auth A].

PF10596
Domain description: U6-snRNA interacting domain of PrP8
Occurring in:
  1. Pre-mRNA-splicing factor 8
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF10596 (U6-snRNA interacting domain of PrP8) in Pre-mRNA-splicing factor 8. Showing 1 copy in chain E [auth A].

PF10597
Domain description: U5-snRNA binding site 2 of PrP8
Occurring in:
  1. Pre-mRNA-splicing factor 8
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF10597 (U5-snRNA binding site 2 of PrP8) in Pre-mRNA-splicing factor 8. Showing 1 copy in chain E [auth A].

PF10598
Domain description: RNA recognition motif of the spliceosomal PrP8
Occurring in:
  1. Pre-mRNA-splicing factor 8
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF10598 (RNA recognition motif of the spliceosomal PrP8) in Pre-mRNA-splicing factor 8. Showing 1 copy in chain E [auth A].

PF08083
Domain description: PROCN (NUC071) domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF08083 (PROCN (NUC071) domain) in Pre-mRNA-splicing factor 8. Showing 1 copy in chain E [auth A].

PF08082
Domain description: PRO8NT (NUC069), PrP8 N-terminal domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
The deposited structure of PDB entry 5gap contains 1 copy of Pfam domain PF08082 (PRO8NT (NUC069), PrP8 N-terminal domain) in Pre-mRNA-splicing factor 8. Showing 1 copy in chain E [auth A] (this domain is out of the observed residue ranges!).

Rfam RNA families (Rfam)
RF00020
Domain description: U5 spliceosomal RNA
Occurring in:
  1. U5 snRNA
The deposited structure of PDB entry 5gap contains 1 copy of Rfam domain RF00020 (U5 spliceosomal RNA) in U5 snRNA. Showing 1 copy in chain C [auth U].

RF00015
Domain description: U4 spliceosomal RNA
Occurring in:
  1. U4 snRNA, 5' region, nucleotides 1-67
The deposited structure of PDB entry 5gap contains 1 copy of Rfam domain RF00015 (U4 spliceosomal RNA) in U4 snRNA, 5' region, nucleotides 1-67. Showing 1 copy in chain A [auth V].

RF00026
Domain description: U6 spliceosomal RNA
Occurring in:
  1. U6 snRNA
The deposited structure of PDB entry 5gap contains 1 copy of Rfam domain RF00026 (U6 spliceosomal RNA) in U6 snRNA. Showing 1 copy in chain B [auth W].

InterPro InterPro annotations
IPR001680
Domain description: WD40 repeat
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP4
IPR003107
Domain description: HAT (Half-A-TPR) repeat
Occurring in:
  1. Pre-mRNA-splicing factor 6
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR011990
Domain description: Tetratricopeptide-like helical domain superfamily
Occurring in:
  1. Pre-mRNA-splicing factor 6
IPR018492
Domain description: Ribosomal protein eL8/Nhp2 family
Occurring in:
  1. 13 kDa ribonucleoprotein-associated protein
IPR002415
Domain description: H/ACA ribonucleoprotein complex, subunit Nhp2-like
Occurring in:
  1. 13 kDa ribonucleoprotein-associated protein
IPR004123
Domain description: Dim1 family
Occurring in:
  1. Spliceosomal protein DIB1
IPR004179
Domain description: Sec63 domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR014001
Domain description: Helicase superfamily 1/2, ATP-binding domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR019734
Domain description: Tetratricopeptide repeat
Occurring in:
  1. Pre-mRNA-splicing factor 6
IPR020472
Domain description: G-protein beta WD-40 repeat
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP4
IPR019775
Domain description: WD40 repeat, conserved site
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP4
IPR001650
Domain description: Helicase, C-terminal domain-like
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR029064
Domain description: Ribosomal protein eL30-like superfamily
Occurring in:
  1. 13 kDa ribonucleoprotein-associated protein
IPR015943
Domain description: WD40/YVTN repeat-like-containing domain superfamily
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP4
IPR002687
Domain description: Nop domain
Occurring in:
  1. Pre-mRNA-processing factor 31
IPR035892
Domain description: C2 domain superfamily
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR014756
Domain description: Immunoglobulin E-set
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR036388
Domain description: Winged helix-like DNA-binding domain superfamily
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR036390
Domain description: Winged helix DNA-binding domain superfamily
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR011545
Domain description: DEAD/DEAH box helicase domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR021983
Domain description: PRP8 domain IV core
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR012337
Domain description: Ribonuclease H-like superfamily
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR004037
Domain description: Large ribosomal subunit protein eL8-like, conserved site
Occurring in:
  1. 13 kDa ribonucleoprotein-associated protein
IPR004038
Domain description: Ribosomal protein eL8/eL30/eS12/Gadd45
Occurring in:
  1. 13 kDa ribonucleoprotein-associated protein
IPR045075
Domain description: Pre-mRNA-splicing factor Syf1-like
Occurring in:
  1. Pre-mRNA-splicing factor 6
IPR010491
Domain description: PRP1 splicing factor, N-terminal
Occurring in:
  1. Pre-mRNA-splicing factor 6
IPR036322
Domain description: WD40-repeat-containing domain superfamily
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP4
IPR014906
Domain description: Pre-mRNA processing factor 4 (PRP4)-like
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP4
IPR010541
Domain description: Small nuclear ribonucleoprotein Prp3, C-terminal domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP3
IPR013881
Domain description: Pre-mRNA-splicing factor 3 domain
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP3
IPR027104
Domain description: U4/U6 small nuclear ribonucleoprotein Prp3
Occurring in:
  1. U4/U6 small nuclear ribonucleoprotein PRP3
IPR019175
Domain description: Prp31 C-terminal
Occurring in:
  1. Pre-mRNA-processing factor 31
IPR042239
Domain description: Nop, C-terminal domain
Occurring in:
  1. Pre-mRNA-processing factor 31
IPR012976
Domain description: NOSIC
Occurring in:
  1. Pre-mRNA-processing factor 31
IPR036070
Domain description: Nop domain superfamily
Occurring in:
  1. Pre-mRNA-processing factor 31
IPR027105
Domain description: U4/U6 small nuclear ribonucleoprotein Prp31
Occurring in:
  1. Pre-mRNA-processing factor 31
IPR036249
Domain description: Thioredoxin-like superfamily
Occurring in:
  1. Spliceosomal protein DIB1
IPR041094
Domain description: Brr2, N-terminal helicase PWI domain
Occurring in:
  1. Pre-mRNA-splicing helicase BRR2
IPR012984
Domain description: PROCT domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR037518
Domain description: MPN domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR000555
Domain description: JAB1/MPN/MOV34 metalloenzyme domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR043173
Domain description: Prp8 RNase domain IV, fingers region
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR043172
Domain description: Prp8 RNase domain IV, palm region
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR019580
Domain description: Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR019581
Domain description: Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR042516
Domain description: Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR019582
Domain description: RNA recognition motif, spliceosomal PrP8
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR012592
Domain description: PROCN domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR012591
Domain description: PRO8NT domain
Occurring in:
  1. Pre-mRNA-splicing factor 8
IPR027652
Domain description: Pre-mRNA-processing-splicing factor 8
Occurring in:
  1. Pre-mRNA-splicing factor 8

Structure domains

CATH CATH domains
3.30.1330.30
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: 60s Ribosomal Protein L30; Chain: A;
Homology: 60s Ribosomal Protein L30; Chain: A;
Occurring in:
  1. 13 kDa ribonucleoprotein-associated protein
The deposited structure of PDB entry 5gap contains 1 copy of CATH domain 3.30.1330.30 (60s Ribosomal Protein L30; Chain: A;) in 13 kDa ribonucleoprotein-associated protein. Showing 1 copy in chain K.
3.40.30.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Glutaredoxin
Homology: Glutaredoxin
Occurring in:
  1. Spliceosomal protein DIB1
The deposited structure of PDB entry 5gap contains 1 copy of CATH domain 3.40.30.10 (Glutaredoxin) in Spliceosomal protein DIB1. Showing 1 copy in chain H [auth D].

Quick links