6J6Q | pdb_00006j6q

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 2.1 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: https://doi.org/10.1016/j.cell.2019.02.006
  • Primary Citation of Related Structures:  
    6J6G, 6J6H, 6J6N, 6J6Q

  • 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 2.9-3.8 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 82,413Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114B [auth C]1,008Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21C [auth J]135Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46D [auth O]451Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45E [auth P]379Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11F [auth Q]364Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2G [auth R]339Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15H [auth S]175Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31I [auth T]157Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22J [auth Z]577Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1K [auth c]590Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1L [auth d]687Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2M [auth I]215Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17N [auth n]455Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1O [auth H]235Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1T [auth v]859Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''U [auth a]111Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'V [auth b]238Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309W [auth t]175Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EGA [auth i],
X [auth u]		94Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1KA [auth z],
Y [auth m]		146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GIA [auth x],
Z [auth j]		77Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FAA [auth h],
HA [auth w]		86Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2BA [auth g],
DA [auth e]		110Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BCA [auth k],
EA [auth s]		196Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3FA [auth l],
JA [auth y]		101Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19LA [auth r],
MA [auth p],
NA [auth q],
OA [auth o]		503Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.2.27
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor YJU2PA [auth F]278Saccharomyces cerevisiae S288CMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP
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QA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP
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RA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN
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EB [auth F]
TA [auth Q]
UA [auth Q]
VA [auth R]
WA [auth T]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AB [auth E]
BB [auth E]
CB [auth E]
DB [auth E]
SA [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		N [auth n]L-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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

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
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary