5YLZ

Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae

Bai, R.Yan, C.Wan, R.Lei, J.Shi, Y.

(2017) Cell 171: 1589-1598.e8

  • DOI: 10.1016/j.cell.2017.10.038
  • Primary Citation of Related Structures:  
    5YLZ

  • PubMed Abstract: 
  • Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3 ...

    Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA. The 3'SS is stabilized through an interaction with the 1585-loop of Prp8. The P complex structure provides a view on splice junction formation critical for understanding the complete splicing cycle.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Shilongshan Road No. 18, Xihu District, Hangzhou 310064, Zhejiang Province, China. Electronic address: shi-lab@tsinghua.edu.cn.



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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114C1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309G175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309NTC25YPR101W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1H859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1NTC90YDR416W
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1I687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1NTC77SYF3YLR117CL2952
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1J590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1NTC85YMR213WYM8261.07
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2K215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2NTC31YGR129W
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31L157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31CWC14YCR063WYCR63WYCR903
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17M [auth T]455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40PRP17SLU4XRS2YDR364CD9481.11
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11N [auth M]364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2SLT11YBR065CYBR0614
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2O [auth N]339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2NTC40SLC3YDL209CD1041
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46P [auth O]451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46CWC1NTC50YPL151CP2594
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15Q [auth P]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45R [auth Q]379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45FUN20YAL032C
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21S [auth R]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21YDR482C
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22T [auth S]577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22YGR278W
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18U251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP18YGR006W
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7V382Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SLU7SLT17YDR088CD4483
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22W1145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP22YER013W
EC: 3.6.4.13
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BX [auth a],
EA [auth h]
196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EY [auth b],
FA [auth i]
94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FZ [auth c],
GA [auth j]
86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
UniProt
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GAA [auth d],
HA [auth k]
77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3BA [auth e],
IA [auth l]
101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1CA [auth f],
JA [auth m]
146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2DA [auth g],
KA [auth n]
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'LA [auth o]238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''MA [auth p]111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]
503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19PSO4YLL036C
EC: 2.3.2.27
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB 214Saccharomyces cerevisiae S288C
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Entity ID: 4
MoleculeChainsLengthOrganismImage
U6 snRNAD 112Saccharomyces cerevisiae S288C
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Entity ID: 5
MoleculeChainsLengthOrganismImage
mRNA/intron lariatE 369Saccharomyces cerevisiae S288C
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Entity ID: 6
MoleculeChainsLengthOrganismImage
U2 snRNAF 1175Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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RA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

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SA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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AB [auth L],
BB [auth L],
CB [auth M],
DB [auth M],
EB [auth N],
AB [auth L],
BB [auth L],
CB [auth M],
DB [auth M],
EB [auth N],
ZA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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TA [auth C],
UA [auth D],
VA [auth D],
WA [auth D],
XA [auth D],
TA [auth C],
UA [auth D],
VA [auth D],
WA [auth D],
XA [auth D],
YA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31430020
Ministry of Science and Technology (China)China2016YFA0501100

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Derived calculations, Other
  • Version 2.0: 2020-10-14
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary