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 

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
  • 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: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP4B465Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP4RNA4YPR178WP9705.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 31C [auth I]494Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP31YGR091W
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 6D [auth G]899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP6RNA6YBR055CYBR0508
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein PRP3E [auth K]469Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP3RNA3YDR473CD8035.16
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosomal protein DIB1F [auth L]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIB1CDH1SNU16YPR082CP9513.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinG [auth M]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114H1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
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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: BRR2RSS1SNU246YER172CSYGP-ORF66
EC: 3.6.4.13
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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: SMD3YLR147CL9634.6
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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: SMB1YER029C
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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: SMD1YGR074W
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2T [auth Q],
M [auth U]
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EN [auth V],
U [auth Y]
94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
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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: SMX3YPR182WP9705.4
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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: SMX2SNP2YFL017W-AYFL017Bw
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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: LSM8YJR022WJ1464YJR83.16
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2Y [auth c]95Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
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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: LSM3SMX4USS2YLR438C-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: LSM6YDR378CD9481.18
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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: LSM5YER146W
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7CA [auth g]115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
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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: LSM4SDB23USS1YER112W
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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

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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