PDBsum entry 7qtt

Splicing

PDB id: 7qtt

Contents

Protein chains

1164 a.a.

70 a.a.

815 a.a.

89 a.a.

198 a.a.

78 a.a.

67 a.a.

84 a.a.

72 a.a.

28 a.a.

792 a.a.

320 a.a.

148 a.a.

100 a.a.

142 a.a.

295 a.a.

285 a.a.

459 a.a.

241 a.a.

306 a.a.

95 a.a.

1936 a.a.

898 a.a.

66 a.a.

70 a.a.

68 a.a.

78 a.a.

68 a.a.

63 a.a.

64 a.a.

159 a.a.

74 a.a.

367 a.a.

DNA/RNA

Ligands

IHP

GTP

Metals

_ZN ×12

_MG ×7

PDB id:

7qtt

Name:

Splicing

Title:

Structural organization of a late activated human spliceosome (baqr, core region)

Structure:

Splicing factor 3b subunit 3. Chain: a. Synonym: pre-mRNA-splicing factor sf3b 130 kda subunit,sf3b130, staf130,spliceosome-associated protein 130,sap 130. Splicing factor 3b subunit 5. Chain: b. Synonym: sf3b5,pre-mRNA-splicing factor sf3b 10 kda subunit. Splicing factor 3b subunit 1. Chain: c.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Unidentified adenovirus. Organism_taxid: 10535. Organism_taxid: 9606

Authors:

C.Cretu,V.Pena

Key ref:

J.Schmitzova et al. Structural basis of catalytic activation in human spl. Nature, . PubMed id: 37165190

Date:

15-Jan-22 Release date: 10-May-23

Protein chain

Q15393  (SF3B3_HUMAN) -  Splicing factor 3B subunit 3 from Homo sapiens

Seq: 1217 a.a.

Struc: 1164 a.a.

Protein chain

Q9BWJ5  (SF3B5_HUMAN) -  Splicing factor 3B subunit 5 from Homo sapiens

Seq: 86 a.a.

Struc: 70 a.a.

Protein chain

O75533  (SF3B1_HUMAN) -  Splicing factor 3B subunit 1 from Homo sapiens

Seq: 1304 a.a.

Struc: 815 a.a.

Protein chain

Q7RTV0  (PHF5A_HUMAN) -  PHD finger-like domain-containing protein 5A from Homo sapiens

Seq: 110 a.a.

Struc: 89 a.a.

Protein chain

Q13435  (SF3B2_HUMAN) -  Splicing factor 3B subunit 2 from Homo sapiens

Seq: 895 a.a.

Struc: 198 a.a.*

Protein chain

Q15427  (SF3B4_HUMAN) -  Splicing factor 3B subunit 4 from Homo sapiens

Seq: 424 a.a.

Struc: 78 a.a.

Protein chain

Q92917  (GPKOW_HUMAN) -  G-patch domain and KOW motifs-containing protein from Homo sapiens

Seq: 476 a.a.

Struc: 67 a.a.

Protein chain

Q15428  (SF3A2_HUMAN) -  Splicing factor 3A subunit 2 from Homo sapiens

Seq: 464 a.a.

Struc: 84 a.a.

Protein chain

Q12874  (SF3A3_HUMAN) -  Splicing factor 3A subunit 3 from Homo sapiens

Seq: 501 a.a.

Struc: 72 a.a.

Protein chain

Q9BRD0  (BUD13_HUMAN) -  BUD13 homolog from Homo sapiens

Seq: 619 a.a.

Struc: 28 a.a.

Protein chain

O60231  (DHX16_HUMAN) -  Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 from Homo sapiens

Seq: 1041 a.a.

Struc: 792 a.a.

Protein chain

O43660  (PLRG1_HUMAN) -  Pleiotropic regulator 1 from Homo sapiens

Seq: 514 a.a.

Struc: 320 a.a.

Protein chain

Q99459  (CDC5L_HUMAN) -  Cell division cycle 5-like protein from Homo sapiens

Seq: 802 a.a.

Struc: 148 a.a.

Protein chain

Q9P013  (CWC15_HUMAN) -  Spliceosome-associated protein CWC15 homolog from Homo sapiens

Seq: 229 a.a.

Struc: 100 a.a.

Protein chain

P41223  (BUD31_HUMAN) -  Protein BUD31 homolog from Homo sapiens

Seq: 144 a.a.

Struc: 142 a.a.

Protein chain

Q9NW64  (RBM22_HUMAN) -  Pre-mRNA-splicing factor RBM22 from Homo sapiens

Seq: 420 a.a.

Struc: 295 a.a.

Protein chain

Q8WUA2  (PPIL4_HUMAN) -  Peptidyl-prolyl cis-trans isomerase-like 4 from Homo sapiens

Seq: 492 a.a.

Struc: 285 a.a.

Protein chain

Q9HCG8  (CWC22_HUMAN) -  Pre-mRNA-splicing factor CWC22 homolog from Homo sapiens

Seq: 908 a.a.

Struc: 459 a.a.

Protein chain

Q9BZJ0  (CRNL1_HUMAN) -  Crooked neck-like protein 1 from Homo sapiens

Seq: 848 a.a.

Struc: 241 a.a.

Protein chain

Q13573  (SNW1_HUMAN) -  SNW domain-containing protein 1 from Homo sapiens

Seq: 536 a.a.

Struc: 306 a.a.*

Protein chain

O15541  (R113A_HUMAN) -  E3 ubiquitin-protein ligase RNF113A from Homo sapiens

Seq: 343 a.a.

Struc: 95 a.a.

Protein chain

Q6P2Q9  (PRP8_HUMAN) -  Pre-mRNA-processing-splicing factor 8 from Homo sapiens

Seq: 2335 a.a.

Struc: 1936 a.a.

Protein chain

Q15029  (U5S1_HUMAN) -  116 kDa U5 small nuclear ribonucleoprotein component from Homo sapiens

Seq: 972 a.a.

Struc: 898 a.a.

Protein chain

P62306  (RUXF_HUMAN) -  Small nuclear ribonucleoprotein F from Homo sapiens

Seq: 86 a.a.

Struc: 66 a.a.

Protein chain

P62304  (RUXE_HUMAN) -  Small nuclear ribonucleoprotein E from Homo sapiens

Seq: 92 a.a.

Struc: 70 a.a.

Protein chain

P62318  (SMD3_HUMAN) -  Small nuclear ribonucleoprotein Sm D3 from Homo sapiens

Seq: 126 a.a.

Struc: 68 a.a.

Protein chain

P62314  (SMD1_HUMAN) -  Small nuclear ribonucleoprotein Sm D1 from Homo sapiens

Seq: 119 a.a.

Struc: 78 a.a.

Protein chain

P62316  (SMD2_HUMAN) -  Small nuclear ribonucleoprotein Sm D2 from Homo sapiens

Seq: 118 a.a.

Struc: 68 a.a.

Protein chain

P62308  (RUXG_HUMAN) -  Small nuclear ribonucleoprotein G from Homo sapiens

Seq: 76 a.a.

Struc: 63 a.a.

Protein chain

P14678  (RSMB_HUMAN) -  Small nuclear ribonucleoprotein-associated proteins B and B' from Homo sapiens

Seq: 240 a.a.

Struc: 64 a.a.

Protein chain

Q9Y3C6  (PPIL1_HUMAN) -  Peptidyl-prolyl cis-trans isomerase-like 1 from Homo sapiens

Seq: 166 a.a.

Struc: 159 a.a.

Protein chain

Q9UQ35  (SRRM2_HUMAN) -  Serine/arginine repetitive matrix protein 2 from Homo sapiens

Seq: 2752 a.a.

Struc: 74 a.a.

Protein chain

Q13356  (PPIL2_HUMAN) -  RING-type E3 ubiquitin-protein ligase PPIL2 from Homo sapiens

Seq: 520 a.a.

Struc: 367 a.a.

* PDB and UniProt seqs differ at 12 residue positions (black crosses)

DNA/RNA chains

G-U-G-C-U-C-G-C-U-U-C-G-G-C-A-G-C-A-C-A-U-A-U-A-C-U-A-A-A-A-U-U-G-G-A-A-C-G-A- 93 bases

G-G-U-U-U-C-U-C-U-U-C-A-G-A-U-C-G-C-A-U-A-A-A-U-C-U-U-U-C-G-C-C-U-U-U-U-A-C-U- 98 bases

A-U-C-G-C-U-U-C-U-C-G-G-C-C-U-G-G-C-U-A-A-G-A-U-C-A-A-G-U-G-U-A-G-U-A-U-C-U-G- 76 bases

U-C-G-G-C-C-U-C-C-G-A-A-C-G-G-U-A-A-G-A-G-C-C-U-A-G-C-A-U-G-U-A-G-A-A-C-U-G-G- 76 bases

Enzyme reactions

• Enzyme class 2: Chain N: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 3: Chains V, p: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)

Peptidylproline (omega=180) (Bound ligand (Het Group name = GTP) matches with 96.88% similarity) = peptidylproline (omega=0)

• Enzyme class 4: Chains Z, u: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site