PDBsum entry 6j6q

Splicing

PDB id: 6j6q

Contents

Protein chains

1913 a.a.

920 a.a.

27 a.a.

357 a.a.

205 a.a.

292 a.a.

261 a.a.

70 a.a.

157 a.a.

447 a.a.

436 a.a.

566 a.a.

102 a.a.

299 a.a.

95 a.a.

722 a.a.

84 a.a.

169 a.a.

156 a.a.

74 a.a.

119 a.a.

75 a.a.

68 a.a.

101 a.a.

100 a.a.

93 a.a.

83 a.a.

108 a.a.

125 a.a.

129 a.a.

161 a.a.

DNA/RNA

Ligands

IHP

GTP

Metals

_MG ×6

_ZN ×7

PDB id:

6j6q

Name:

Splicing

Title:

Cryo-em structure of the yeast b -B2 complex at an average resolution of 3.7 angstrom

Structure:

Pre-mRNA-splicing factor 8. Chain: a. Pre-mRNA-splicing factor snu114. Chain: c. Synonym: 114 kda u5 small nuclear ribonucleoprotein component,growth inhibitory protein 10. Pre-mRNA-splicing factor cwc21. Chain: j. Synonym: complexed with cef1 protein 21.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Synthetic: yes. Saccharomyces cerevisiae s288c. Strain: atcc 204508 / s288c

Authors:

R.Wan,R.Bai,C.Yan,J.Lei,Y.Shi

Key ref:

R.Wan et al. (2019). Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Cell, 177, 339. PubMed id: 30879786 DOI: 10.1016/j.cell.2019.02.006

Date:

15-Jan-19 Release date: 24-Apr-19

Protein chain

P33334  (PRP8_YEAST) -  Pre-mRNA-splicing factor 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 2413 a.a.

Struc: 1913 a.a.

Protein chain

P36048  (SN114_YEAST) -  Pre-mRNA-splicing factor SNU114 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1008 a.a.

Struc: 920 a.a.

Protein chain

Q03375  (CWC21_YEAST) -  Pre-mRNA-splicing factor CWC21 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 135 a.a.

Struc: 27 a.a.

Protein chain

Q12417  (PRP46_YEAST) -  Pre-mRNA-splicing factor PRP46 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 451 a.a.

Struc: 357 a.a.

Protein chain

P28004  (PRP45_YEAST) -  Pre-mRNA-processing protein 45 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 379 a.a.

Struc: 205 a.a.

Protein chain

P38241  (SLT11_YEAST) -  Pre-mRNA-splicing factor SLT11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 364 a.a.

Struc: 292 a.a.

Protein chain

Q12046  (CWC2_YEAST) -  Pre-mRNA-splicing factor CWC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 339 a.a.

Struc: 261 a.a.

Protein chain

Q03772  (CWC15_YEAST) -  Pre-mRNA-splicing factor CWC15 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 175 a.a.

Struc: 70 a.a.*

Protein chain

P25337  (BUD31_YEAST) -  Pre-mRNA-splicing factor BUD31 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 157 a.a.

Struc: 157 a.a.

Protein chain

P53333  (CWC22_YEAST) -  Pre-mRNA-splicing factor CWC22 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 577 a.a.

Struc: 447 a.a.

Protein chain

Q03654  (CEF1_YEAST) -  Pre-mRNA-splicing factor CEF1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 590 a.a.

Struc: 436 a.a.

Protein chain

Q12309  (CLF1_YEAST) -  Pre-mRNA-splicing factor CLF1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 687 a.a.

Struc: 566 a.a.

Protein chain

P53277  (SYF2_YEAST) -  Pre-mRNA-splicing factor SYF2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 102 a.a.

Protein chain

P40968  (PRP17_YEAST) -  Pre-mRNA-processing factor 17 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 455 a.a.

Struc: 299 a.a.

Protein chain

P21374  (ISY1_YEAST) -  Pre-mRNA-splicing factor ISY1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 235 a.a.

Struc: 95 a.a.

Protein chain

Q04048  (SYF1_YEAST) -  Pre-mRNA-splicing factor SYF1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 859 a.a.

Struc: 722 a.a.

Protein chain

P40567  (MSL1_YEAST) -  U2 small nuclear ribonucleoprotein B'' from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 111 a.a.

Struc: 84 a.a.

Protein chain

Q08963  (RU2A_YEAST) -  U2 small nuclear ribonucleoprotein A' from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 238 a.a.

Struc: 169 a.a.

Protein chain

Q06091  (SN309_YEAST) -  Pre-mRNA-splicing factor SNT309 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 175 a.a.

Struc: 156 a.a.

Protein chains

Q12330  (RUXE_YEAST) -  Small nuclear ribonucleoprotein E from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 94 a.a.

Struc: 74 a.a.

Protein chain

Q02260  (SMD1_YEAST) -  Small nuclear ribonucleoprotein Sm D1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 146 a.a.

Struc: 119 a.a.

Protein chains

P40204  (RUXG_YEAST) -  Small nuclear ribonucleoprotein G from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 77 a.a.

Struc: 75 a.a.

Protein chains

P54999  (RUXF_YEAST) -  Small nuclear ribonucleoprotein F from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 86 a.a.

Struc: 68 a.a.

Protein chains

Q06217  (SMD2_YEAST) -  Small nuclear ribonucleoprotein Sm D2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 110 a.a.

Struc: 101 a.a.

Protein chain

P40018  (RSMB_YEAST) -  Small nuclear ribonucleoprotein-associated protein B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 196 a.a.

Struc: 100 a.a.

Protein chain

P40018  (RSMB_YEAST) -  Small nuclear ribonucleoprotein-associated protein B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 196 a.a.

Struc: 93 a.a.

Protein chains

P43321  (SMD3_YEAST) -  Small nuclear ribonucleoprotein Sm D3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 101 a.a.

Struc: 83 a.a.

Protein chain

Q02260  (SMD1_YEAST) -  Small nuclear ribonucleoprotein Sm D1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 146 a.a.

Struc: 108 a.a.

Protein chains

P32523  (PRP19_YEAST) -  Pre-mRNA-processing factor 19 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 503 a.a.

Struc: 125 a.a.

Protein chain

P32523  (PRP19_YEAST) -  Pre-mRNA-processing factor 19 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 503 a.a.

Struc: 129 a.a.

Protein chain

P28320  (CWC16_YEAST) -  Splicing factor YJU2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 278 a.a.

Struc: 161 a.a.

* PDB and UniProt seqs differ at 29 residue positions (black crosses)

DNA/RNA chains

G-U-G-A-U-C-U-A-G-A-A-A-G-G-U-A-U-G-U-C-U-A-A-A-G-U-U-A-C-U-U-A-U-G-C-U-C-U-U- 57 bases

A-A-G-C-A-G-C-U-U-U-A-C-A-G-A-U-C-A-A-U-G-G-C-G-G-A-G-G-G-A-G-G-U-C-A-A-C-A-U- 179 bases

G-U-U-C-G-C-G-A-A-G-U-A-A-C-C-C-U-U-C-G-U-G-G-A-C-A-U-U-U-G-G-U-C-A-A-U-U-U-G- 103 bases

A-C-G-A-A-U-C-U-C-U-U-U-G-C-C-U-U-U-U-G-G-C-U-U-A-G-A-U-C-A-A-G-U-G-U-A-G-U-A- 210 bases

Enzyme reactions

• Enzyme class: Chains r, p, q, o: 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

DOI no: 10.1016/j.cell.2019.02.006

Cell 177:339 (2019)

PubMed id: 30879786

Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.

R.Wan, R.Bai, C.Yan, J.Lei, Y.Shi.

ABSTRACT

Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B^∗) is pivotal for understanding the branching reaction. In this study, we assembled the B^∗ complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B^∗ complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B^∗ complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state.