5GM6

Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a yeast activated spliceosome at 3.5 angstrom resolution

Yan, C.Wan, R.Bai, R.Huang, G.Shi, Y.

(2016) Science 353: 904-911

  • DOI: 10.1126/science.aag0291
  • Primary Citation of Related Structures:  
    5GM6

  • PubMed Abstract: 
  • Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3 ...

    Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. shi-lab@tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A2287Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2B2163Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRR2RSS1SNU246YER172CSYGP-ORF66
EC: 3.6.4.13
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114C1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RSE1F1361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSE1SAP130YML049CYM9827.03C
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Entity ID: 7
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Cold sensitive U2 snRNA suppressor 1G [auth H]436Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CUS1YMR240CYM9408.02C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP11H [auth I]266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP11PRP10RNA11YDL043CD2711
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RDS3I [auth J]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RDS3YPR094WP9513.2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RDS3 complex subunit 10J [auth K]85Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YSF3RCP10YNL138W-A
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Entity ID: 14
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Pre-mRNA-splicing factor PRP46N [auth O]451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46CWC1NTC50YPL151CP2594
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Entity ID: 15
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Pre-mRNA-processing protein 45O [auth P]379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45FUN20YAL032C
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Entity ID: 16
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Pre-mRNA-splicing factor SLT11P [auth Q]364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2SLT11YBR065CYBR0614
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Entity ID: 17
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Pre-mRNA-splicing factor CWC2Q [auth R]339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2NTC40SLC3YDL209CD1041
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Entity ID: 18
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Pre-mRNA-splicing factor CWC15R [auth S]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31S [auth T]157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31CWC14YCR063WYCR63WYCR903
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Entity ID: 20
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Pre-mRNA leakage protein 1T [auth U]207Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PML1YLR016CL1591
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U2 snRNP component IST3U [auth V]148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IST3SNU17YIR005WYIB5W
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Entity ID: 22
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Pre-mRNA-splicing factor CWC26V [auth W]266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD13CWC26SLC7YGL174WG1642
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Entity ID: 23
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Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2W [auth Y]876Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP2RNA2YNR011CN2048
EC: 3.6.4.13
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Entity ID: 24
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Pre-mRNA-splicing factor CWC22X [auth Z]577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22YGR278W
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Entity ID: 25
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Pre-mRNA-splicing factor CWC24Y [auth a]259Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC24YLR323CL8543.3
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl isomerase CWC27Z [auth b]301Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC27CYP7YPL064C
EC: 5.2.1.8
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Entity ID: 27
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Pre-mRNA-splicing factor CEF1AA [auth c]587Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1
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Entity ID: 28
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U2 snRNP component HSH155BA [auth G]971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSH155YMR288WYM8021.14
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Pre-mRNA-splicing factor CLF1CA [auth d]687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1
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Pre-mRNA-splicing factor CWC21DA [auth X]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21YDR482C
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Entity ID: 31
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Pre-mRNA-splicing factor SYF1EA [auth v]859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1
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Protein HSH49FA [auth e]213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSH49YOR319WO6142
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Entity ID: 33
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Pre-mRNA-splicing factor SYF2GA [auth f]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2NTC31YGR129W
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Entity ID: 34
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Pre-mRNA-processing factor 19HA [auth o],
IA [auth p],
JA [auth q],
KA [auth r]
503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19PSO4YLL036C
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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Entity ID: 35
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Pre-mRNA-splicing factor SNT309LA [auth t]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309NTC25YPR101W
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Pre-mRNA-processing factor 17MA [auth n]455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40PRP17SLU4XRS2YDR364CD9481.11
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Small nuclear ribonucleoprotein-associated protein BNA [auth k]196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
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Small nuclear ribonucleoprotein EOA [auth i]94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
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Small nuclear ribonucleoprotein FPA [auth h]86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
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Small nuclear ribonucleoprotein GQA [auth j]77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
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Small nuclear ribonucleoprotein Sm D3RA [auth l]101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
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Small nuclear ribonucleoprotein Sm D1SA [auth m]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
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Small nuclear ribonucleoprotein Sm D2TA [auth g]94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
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Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequenceD 214Saccharomyces cerevisiae
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Saccharomyces cerevisiae strain T.52_2H chromosome XII sequenceE 112Saccharomyces cerevisiae
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U2 snRNAK [auth L]1175Saccharomyces cerevisiae S288C
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Entity ID: 12
MoleculeChainsLengthOrganismImage
Pre-mRNAL [auth N]25Saccharomyces cerevisiae S288C
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsLengthOrganismImage
Pre-mRNAM 61Saccharomyces cerevisiae S288C
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
UA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ADP
Query on ADP

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KB [auth Y]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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AB [auth J],
BB [auth J],
CB [auth J],
DB [auth Q],
EB [auth Q],
AB [auth J],
BB [auth J],
CB [auth J],
DB [auth Q],
EB [auth Q],
FB [auth R],
GB [auth T],
HB [auth T],
IB [auth T],
LB [auth a],
MB [auth a],
NB [auth a],
ZA [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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JB [auth Y],
VA [auth E],
WA [auth E],
XA [auth E],
YA [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Other
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other