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)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: 2
MoleculeChainsSequence LengthOrganismDetails
U4/U6 small nuclear ribonucleoprotein PRP4
B
465Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)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: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
R, J
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: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
S, O
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: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
T, P
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: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
U, Q
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: 14
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
V, Y
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: 15
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
W, Z
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: 16
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
X, a
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: 17
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
b
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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)Mutation(s): 0 
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
Download SDF File 
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

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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