6J6G

Cryo-EM structure of the yeast B*-a2 complex at an average resolution of 3.2 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Structures With Same Primary Citation

  • 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 t ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114C1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36048 
Go to UniProtKB:  P36048
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC21J135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21YDR482C
Find proteins for Q03375 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03375 
Go to UniProtKB:  Q03375
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor PRP46O451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46CWC1NTC50YPL151CP2594
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12417 
Go to UniProtKB:  Q12417
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing protein 45P379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45FUN20YAL032C
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28004 
Go to UniProtKB:  P28004
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SLT11Q364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2SLT11YBR065CYBR0614
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38241 
Go to UniProtKB:  P38241
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC2R339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2NTC40SLC3YDL209CD1041
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12046 
Go to UniProtKB:  Q12046
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC15S175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03772 
Go to UniProtKB:  Q03772
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor BUD31T157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31CWC14YCR063WYCR63WYCR903
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25337 
Go to UniProtKB:  P25337
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22Z577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22YGR278W
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53333 
Go to UniProtKB:  P53333
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CEF1c590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1NTC85YMR213WYM8261.07
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03654 
Go to UniProtKB:  Q03654
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CLF1d687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1NTC77SYF3YLR117CL2952
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12309 
Go to UniProtKB:  Q12309
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF2I215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2NTC31YGR129W
Find proteins for P53277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53277 
Go to UniProtKB:  P53277
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17n455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40PRP17SLU4XRS2YDR364CD9481.11
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40968 
Go to UniProtKB:  P40968
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor ISY1H235Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ISY1NTC30UTR3YJR050WJ1657
Find proteins for P21374 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21374 
Go to UniProtKB:  P21374
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1v859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1NTC90YDR416W
Find proteins for Q04048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04048 
Go to UniProtKB:  Q04048
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''a111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40567 
Go to UniProtKB:  P40567
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'b238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08963 
Go to UniProtKB:  Q08963
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNT309t175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309NTC25YPR101W
Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06091 
Go to UniProtKB:  Q06091
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Ei, u94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12330 
Go to UniProtKB:  Q12330
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1m, z146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02260 
Go to UniProtKB:  Q02260
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Gj, x77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40204 
Go to UniProtKB:  P40204
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Fh, w86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54999 
Go to UniProtKB:  P54999
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2e, g110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06217 
Go to UniProtKB:  Q06217
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein Bk, s196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40018 
Go to UniProtKB:  P40018
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3l, y101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43321 
Go to UniProtKB:  P43321
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19o, p, q, r503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19PSO4YLL036C
EC: 2.3.2.27
Find proteins for P32523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32523 
Go to UniProtKB:  P32523
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 16
MoleculeChainsLengthOrganism
ACT1 pre-mRNAB679Saccharomyces cerevisiae S288C

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 17
MoleculeChainsLengthOrganism
U5 snRNAD214Saccharomyces cerevisiae S288C

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 18
MoleculeChainsLengthOrganism
U6 snRNAE112Saccharomyces cerevisiae S288C

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 19
MoleculeChainsLengthOrganism
U2 snRNAL1175Saccharomyces cerevisiae S288C
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6P
Query on I6P

Download CCD File 
A
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

Download CCD File 
C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
Q, R, T
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other