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
  • Structures With Same Primary Citation

  • 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: 4
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP4
H
465Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20053

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 6
J
899Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P19735

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP3
G
469Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03338

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Unknown protein
x
100Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
b, k
196Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
d, n
101Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
e, p
94Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Snu66
E
328Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12420

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
2
95Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38203

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
4
187Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40070

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
6
86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06406

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
h, l
146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
j, m
110Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
f, q
86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
g, r
77Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein
K
126Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39990

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
3
89Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P57743

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
5
93Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40089

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
7
115Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53905

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
8
109Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47093

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
C
1008Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36048

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Spliceosomal protein DIB1
D
143Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06819

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 31
F
494Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49704

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
B
2163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32639

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 19
MoleculeChainsLengthOrganism
U5 snRNAU214Saccharomyces cerevisiae

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
U4 snRNAV160Saccharomyces cerevisiae

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
U6 snRNAW112Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
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 

  • 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