5GAO

Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution.

Nguyen, T.H., Galej, W.P., Bai, X.C., Oubridge, C., Newman, A.J., Scheres, S.H., Nagai, K.

(2016) Nature 530: 298-302

  • DOI: 10.1038/nature16940
  • Primary Citation of Related Structures:  
  • Also Cited By: 5MQ0, 5MPS

  • PubMed Abstract: 

    • U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 p ...

    U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.

    Related Citations: 
    • The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
      Nguyen, T.H.D.,Galej, W.,Bai, X.C.,Savva, C.G.,Newman, A.J.,Scheres, S.H.W.,Nagai, K.
      (2015) Nature 523: 47

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
k
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
l
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
m
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
n
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
p
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
q
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
r
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Snu66
E
338Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU66
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12420
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
B
2163Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BRR2 (RSS1, SNU246)
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32639
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
267Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Entity ID: 10
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequenceV96Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 2018-10-03
    Type: Data collection, Refinement description