Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 30-mer - A2BCDEFGH1IJKLMNOPQRSTUVW Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 30-mer - A21BCDEFGHIJ 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1373.83 kDa 
• Atom Count: 58253 
• Residue Count: 8679 
• Unique protein chains: 23
• Unique nucleic acid chains: 4

3JCM

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

• DOI: 10.2210/pdb3JCM/pdb
• EMDataResource: EMD-6561

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
• Mutation(s): No 


• Deposited: 2015-12-23 Released: 2016-02-24 
• Deposition Author(s): Wan, R., Yan, C., Bai, R., Wang, L., Huang, M., Wong, C.C., Shi, Y.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 26743623 
• DOI: 10.1126/science.aad6466
• Structures With Same Primary Citation


• 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 (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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing factor 8	A	2413	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P33334

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
U4/U6 small nuclear ribonucleoprotein PRP4	B	465	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRP4, RNA4, YPR178W, P9705.6
Find proteins for P20053 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P20053

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-processing factor 31	I	494	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRP31, YGR091W
Find proteins for P49704 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P49704

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing factor 6	G	899	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRP6, RNA6, YBR055C, YBR0508
Find proteins for P19735 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P19735

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
U4/U6 small nuclear ribonucleoprotein PRP3	K	469	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRP3, RNA3, YDR473C, D8035.16
Find proteins for Q03338 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q03338

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Spliceosomal protein DIB1	L	143	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: DIB1, CDH1, SNU16, YPR082C, P9513.12
Find proteins for Q06819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q06819

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
13 kDa ribonucleoprotein-associated protein	M	126	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SNU13, YEL026W
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P39990

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing factor SNU114	H	1008	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SNU114, GIN10, YKL173W, YKL637
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P36048

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
Pre-mRNA-splicing helicase BRR2	N	2163	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: BRR2, RSS1, SNU246, YER172C, SYGP-ORF66 EC: 3.6.4.13
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P32639

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein Sm D3	J, R	101	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SMD3, YLR147C, L9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P43321

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein-associated protein B	O, S	196	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SMB1, YER029C
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P40018

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein Sm D1	P, T	146	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SMD1, YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02260

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein Sm D2	Q, U	110	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SMD2, YLR275W, L9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q06217

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein E	V, Y	94	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SME1, YOR159C
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q12330

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein F	W, Z	86	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SMX3, YPR182W, P9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P54999

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
Small nuclear ribonucleoprotein G	X, a	77	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SMX2, SNP2, YFL017W-A, YFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P40204

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
U6 snRNA-associated Sm-like protein LSm8	b	109	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM8, YJR022W, J1464, YJR83.16
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P47093

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
U6 snRNA-associated Sm-like protein LSm2	c	95	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM2, SMX5, SNP3, YBL026W, YBL0425
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38203

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
U6 snRNA-associated Sm-like protein LSm3	d	89	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM3, SMX4, USS2, YLR438C-A
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P57743

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
U6 snRNA-associated Sm-like protein LSm6	e	86	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM6, YDR378C, D9481.18
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q06406

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
U6 snRNA-associated Sm-like protein LSm5	f	93	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM5, YER146W
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P40089

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
U6 snRNA-associated Sm-like protein LSm7	g	115	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM7, YNL147W, N1202, N1780
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P53905

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
U6 snRNA-associated Sm-like protein LSm4	h	187	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM4, SDB23, USS1, YER112W
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P40070

Entity ID: 24
Molecule	Chains	Length	Organism
pre-mRNA	C	20	synthetic construct

Entity ID: 25
Molecule	Chains	Length	Organism
SNR6 snRNA	D	112	Saccharomyces cerevisiae S288C

Entity ID: 26
Molecule	Chains	Length	Organism
SNR14 snRNA	E	160	Saccharomyces cerevisiae S288C

Entity ID: 27
Molecule	Chains	Length	Organism
SNR7-L snRNA	F	214	Saccharomyces cerevisiae S288C

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	H	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
M7M	E	N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) C13 H23 N5 O11 P2 DHQQIEJARUGVNZ-WOUKDFQISA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-23 
• Released Date: 2016-02-24 
Deposition Author(s): Wan, R., Yan, C., Bai, R., Wang, L., Huang, M., Wong, C.C., Shi, Y.

Revision History 

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references, Derived calculations, Other