3JCM

Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


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Literature

The 3.8 angstrom structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis

Wan, R.Yan, C.Bai, R.Wang, L.Huang, M.Wong, C.C.Shi, Y.

(2016) Science 351: 466-475

  • DOI: 10.1126/science.aad6466

  • PubMed Abstract: 
  • Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which comprises the U5 small nuclear ribonucleoprotein (sn ...

    Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which comprises the U5 small nuclear ribonucleoprotein (snRNP), the U4 and U6 small nuclear RNA (snRNA) duplex, and a number of protein factors. Here we report the three-dimensional structure of a Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at an overall resolution of 3.8 angstroms by single-particle electron cryomicroscopy. The local resolution for the core regions of the tri-snRNP reaches 3.0 to 3.5 angstroms, allowing construction of a refined atomic model. Our structure contains U5 snRNA, the extensively base-paired U4/U6 snRNA, and 30 proteins including Prp8 and Snu114, which amount to 8495 amino acids and 263 nucleotides with a combined molecular mass of ~1 megadalton. The catalytic nucleotide U80 from U6 snRNA exists in an inactive conformation, stabilized by its base-pairing interactions with U4 snRNA and protected by Prp3. Pre-messenger RNA is bound in the tri-snRNP through base-pairing interactions with U6 snRNA and loop I of U5 snRNA. This structure, together with that of the spliceosome, reveals the molecular choreography of the snRNAs in the activation process of the spliceosomal ribozyme.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 8
A
2413Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP8 (DBF3, DNA39, RNA8, SLT21, USA2)
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33334
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP4
B
465Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP4 (RNA4)
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20053
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 31
I
494Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP31
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49704
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor 6
G
899Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP6 (RNA6)
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P19735
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP3
K
469Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP3 (RNA3)
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03338
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Spliceosomal protein DIB1
L
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: DIB1 (CDH1, SNU16)
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06819
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein
M
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNU13
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SNU13
Go to UniProtKB:  P39990
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SNU114
H
1008Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNU114 (GIN10)
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36048
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing helicase BRR2
N
2163Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
R, J
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
S, O
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
T, P
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
U, Q
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
V, Y
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
W, Z
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
X, a
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
b
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM8
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM8
Go to UniProtKB:  P47093
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
c
95Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM2 (SMX5, SNP3)
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM2
Go to UniProtKB:  P38203
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
d
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM3 (SMX4, USS2)
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM3
Go to UniProtKB:  P57743
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
e
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM6
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM6
Go to UniProtKB:  Q06406
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
f
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM5
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM5
Go to UniProtKB:  P40089
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
g
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM7
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM7
Go to UniProtKB:  P53905
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
h
187Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM4 (SDB23, USS1)
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM4
Go to UniProtKB:  P40070
Entity ID: 24
MoleculeChainsLengthOrganism
pre-mRNAC20synthetic construct
Entity ID: 25
MoleculeChainsLengthOrganism
SNR6 snRNAD112Saccharomyces cerevisiae S288C
Entity ID: 26
MoleculeChainsLengthOrganism
SNR14 snRNAE160Saccharomyces cerevisiae S288C
Entity ID: 27
MoleculeChainsLengthOrganism
SNR7-L snRNAF214Saccharomyces cerevisiae S288C
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
H
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
M7M
Query on M7M

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Download CCD File 
E
N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)
C13 H23 N5 O11 P2
DHQQIEJARUGVNZ-WOUKDFQISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release