3JCM

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

Experimental Data Snapshot

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

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This is version 1.1 of the entry. See complete history. 


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
  • Primary Citation of Related Structures:  
    3JCM

  • 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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4B465Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP4, RNA4, YPR178W, P9705.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31C [auth I]494Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP31, YGR091W
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6D [auth G]899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP6, RNA6, YBR055C, YBR0508
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3E [auth K]469Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP3, RNA3, YDR473C, D8035.16
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosomal protein DIB1F [auth L]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIB1, CDH1, SNU16, YPR082C, P9513.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinG [auth M]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13, YEL026W
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Entity ID: 8
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Pre-mRNA-splicing factor SNU114H1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114, GIN10, YKL173W, YKL637
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Entity ID: 9
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Pre-mRNA-splicing helicase BRR2I [auth N]2163Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRR2, RSS1, SNU246, YER172C, SYGP-ORF66
EC: 3.6.4.13
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Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3Q [auth J],
J [auth R]		101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3, YLR147C, L9634.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BR [auth O],
K [auth S]		196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1, YER029C
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1S [auth P],
L [auth T]		146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1, YGR074W
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Entity ID: 13
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Small nuclear ribonucleoprotein Sm D2T [auth Q],
M [auth U]		110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2, YLR275W, L9328.5
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Entity ID: 14
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Small nuclear ribonucleoprotein EN [auth V],
U [auth Y]		94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1, YOR159C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FO [auth W],
V [auth Z]		86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3, YPR182W, P9705.4
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GP [auth X],
W [auth a]		77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2, SNP2, YFL017W-A, YFL017Bw
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8X [auth b]109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM8, YJR022W, J1464, YJR83.16
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Entity ID: 18
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U6 snRNA-associated Sm-like protein LSm2Y [auth c]95Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM2, SMX5, SNP3, YBL026W, YBL0425
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3Z [auth d]89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM3, SMX4, USS2, YLR438C-A
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6AA [auth e]86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6, YDR378C, D9481.18
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5BA [auth f]93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5, YER146W
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Entity ID: 22
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U6 snRNA-associated Sm-like protein LSm7CA [auth g]115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7, YNL147W, N1202, N1780
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4DA [auth h]187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4, SDB23, USS1, YER112W
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Entity ID: 24
MoleculeChainsLengthOrganismImage
pre-mRNAEA [auth C]20synthetic construct
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Entity ID: 25
MoleculeChainsLengthOrganismImage
SNR6 snRNAFA [auth D]112Saccharomyces cerevisiae S288C
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Entity ID: 26
MoleculeChainsLengthOrganismImage
SNR14 snRNAGA [auth E]160Saccharomyces cerevisiae S288C
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Entity ID: 27
MoleculeChainsLengthOrganismImage
SNR7-L snRNAHA [auth F]214Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
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IA [auth H]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
M7M
Query on M7M
Download Ideal Coordinates CCD File 
JA [auth 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: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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