5GAO

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 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:  
    5GAM, 5GAN, 5GAO, 5GAP

  • 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 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs) ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BA [auth k]196Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40018
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1B [auth l]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2C [auth m]110Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3D [auth n]101Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EE [auth p]94Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FF [auth q]86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GG [auth r]77Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Snu66H [auth E]338Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2I [auth B]2,163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8K [auth A]267Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequenceJ [auth V]96Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 2018-10-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-10-02
    Changes: Data collection, Other