6J6Q

Cryo-EM structure of the yeast B*-b2 complex at an average resolution of 3.7 angstrom

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

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

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

(2019) Cell 177: 339-351.e13

  • DOI: 10.1016/j.cell.2019.02.006
  • Primary Citation of Related Structures:  
    6J6N, 6J6Q, 6J6G, 6J6H

  • PubMed 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 ...

    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.

    Organizational Affiliation: 

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China. Electronic address: shi-lab@tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8 A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
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Pre-mRNA-splicing factor SNU114 C1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114, GIN10, YKL173W, YKL637
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
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Pre-mRNA-splicing factor CWC21 J135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21, YDR482C
Find proteins for Q03375 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46 O451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46, CWC1, NTC50, YPL151C, P2594
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45 P379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45, FUN20, YAL032C
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11 Q364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2, SLT11, YBR065C, YBR0614
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
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Pre-mRNA-splicing factor CWC2 R339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2, NTC40, SLC3, YDL209C, D1041
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
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Pre-mRNA-splicing factor CWC15 S175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15, YDR163W, YD8358.17
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Entity ID: 9
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Pre-mRNA-splicing factor BUD31 T157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31, CWC14, YCR063W, YCR63W, YCR903
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Entity ID: 10
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Pre-mRNA-splicing factor CWC22 Z577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22, YGR278W
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Entity ID: 11
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Pre-mRNA-splicing factor CEF1 c590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1, NTC85, YMR213W, YM8261.07
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Entity ID: 12
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Pre-mRNA-splicing factor CLF1 d687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1, NTC77, SYF3, YLR117C, L2952
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Entity ID: 13
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Pre-mRNA-splicing factor SYF2 I215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2, NTC31, YGR129W
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17 n455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40, PRP17, SLU4, XRS2, YDR364C, D9481.11
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
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Pre-mRNA-splicing factor ISY1 H235Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ISY1, NTC30, UTR3, YJR050W, J1657
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Entity ID: 20
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Pre-mRNA-splicing factor SYF1 v859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1, NTC90, YDR416W
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Entity ID: 21
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U2 small nuclear ribonucleoprotein B'' a111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1, YIR009W, YIB9W
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
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U2 small nuclear ribonucleoprotein A' b238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1, YPL213W
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
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Pre-mRNA-splicing factor SNT309 t175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309, NTC25, YPR101W
Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
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Small nuclear ribonucleoprotein E i, u94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1, YOR159C
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Entity ID: 25
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Small nuclear ribonucleoprotein Sm D1 m, z146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1, YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
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Small nuclear ribonucleoprotein G j, x77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2, SNP2, YFL017W-A, YFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
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Small nuclear ribonucleoprotein F h, w86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3, YPR182W, P9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
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Small nuclear ribonucleoprotein Sm D2 e, g110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2, YLR275W, L9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
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Small nuclear ribonucleoprotein-associated protein B k, s196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1, YER029C
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Entity ID: 30
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Small nuclear ribonucleoprotein Sm D3 l, y101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3, YLR147C, L9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
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Pre-mRNA-processing factor 19 o, p, q, r503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19, PSO4, YLL036C
EC: 2.3.2.27
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor YJU2 F278Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YJU2, CWC16, YKL095W, YKL442
Find proteins for P28320 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsLengthOrganismImage
UBC4 pre-mRNAB246Saccharomyces cerevisiae S288C
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Entity ID: 17
MoleculeChainsLengthOrganismImage
U5 snRNAD214Saccharomyces cerevisiae S288C
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Entity ID: 18
MoleculeChainsLengthOrganismImage
U6 snRNAE112Saccharomyces cerevisiae S288C
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Entity ID: 19
MoleculeChainsLengthOrganismImage
U2 snRNAL1175Saccharomyces cerevisiae S288C
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		nL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31430020
National Natural Science Foundation of ChinaChina31621092
Ministry of Science and Technology (China)China2016YFA0501100

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2020-10-14
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary