5ZWN

Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: CELL 
  • 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 fully assembledSaccharomyces cerevisiaespliceosome before activation

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

(2018) Science 360: 1423-1429

  • DOI: 10.1126/science.aau0325
  • Primary Citation of Related Structures:  
    5ZWM, 5ZWO, 5ZWN

  • PubMed Abstract: 
  • The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, r ...

    The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.


    Organizational Affiliation

    Institute of Biology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310064, Zhejiang Province, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDa homologQ300Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNP1YIL061C
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00916 
Go to UniProtKB:  Q00916
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein CR231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YHC1YLR298CL8003.21
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05900 
Go to UniProtKB:  Q05900
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AS298Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MUD1YBR119WYBR0915
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32605 
Go to UniProtKB:  P32605
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component PRP42T544Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP42MUD16SNU65YDR235WYD8419.02
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03776 
Go to UniProtKB:  Q03776
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 39U629Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP39YML046WYM9827.06
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39682 
Go to UniProtKB:  P39682
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NAM8V523Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAM8MRE2YHR086W
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00539 
Go to UniProtKB:  Q00539
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
56 kDa U1 small nuclear ribonucleoprotein componentW492Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU56MUD10YDR240C
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03782 
Go to UniProtKB:  Q03782
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein Ba196Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1b146Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2c110Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3d101Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Ee94Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Ff86Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Gg77Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component SNU71X619Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU71YGR013W
Find proteins for P53207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53207 
Go to UniProtKB:  P53207
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LUC7Y261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LUC7EPE1EXM2YDL087C
Find proteins for Q07508 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07508 
Go to UniProtKB:  Q07508
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
U1 snRNPx49Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing ATP-dependent RNA helicase PRP28y588Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP28YDR243CYD8419.10C
EC: 3.6.4.13
Find proteins for P23394 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23394 
Go to UniProtKB:  P23394
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
pre-mRNAG22Saccharomyces cerevisiae S288C
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
U1 snRNAP568Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
R, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: CELL 
  • 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: 2018-08-29
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other