5GAN

The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 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 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8C [auth A]2413Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4D [auth H]465Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20053 
Go to UniProtKB:  P20053
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6E [auth J]899Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P19735 
Go to UniProtKB:  P19735
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosomal protein DIB1F [auth D]143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06819 
Go to UniProtKB:  Q06819
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31G [auth F]494Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49704 
Go to UniProtKB:  P49704
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3H [auth G]469Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03338 
Go to UniProtKB:  Q03338
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2I [auth B]2163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32639 
Go to UniProtKB:  P32639
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinJ [auth x]100Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BS [auth b], K [auth k]196Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1X [auth h], L [auth l]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2Y [auth j], M [auth m]110Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3W [auth d], N [auth n]101Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ET [auth e], O [auth p]94Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FU [auth f], P [auth q]86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GV [auth g], Q [auth r]77Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Snu66R [auth E]328Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12420 
Go to UniProtKB:  Q12420
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinAA [auth K]126Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39990 
Go to UniProtKB:  P39990
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2BA [auth 2]95Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38203 
Go to UniProtKB:  P38203
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3CA [auth 3]89Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P57743 
Go to UniProtKB:  P57743
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4DA [auth 4]187Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40070 
Go to UniProtKB:  P40070
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5EA [auth 5]93Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40089 
Go to UniProtKB:  P40089
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6FA [auth 6]86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06406 
Go to UniProtKB:  Q06406
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7GA [auth 7]115Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53905 
Go to UniProtKB:  P53905
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8HA [auth 8]109Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47093 
Go to UniProtKB:  P47093
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114IA [auth C]1008Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36048 
Go to UniProtKB:  P36048
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
U4 snRNAA [auth V]160Saccharomyces cerevisiae
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
U6 snRNAB [auth W]112Saccharomyces cerevisiae
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsLengthOrganismImage
U5 snRNAZ [auth U]214Saccharomyces cerevisiae
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
JA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




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: 2017-08-30
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-03-21
    Changes: Other, Structure summary
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other