5Y88

Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 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 an Intron Lariat Spliceosome from Saccharomyces cerevisiae

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

(2017) Cell 171: 120-132

  • DOI: 10.1016/j.cell.2017.08.029
  • Primary Citation of Related Structures:  
    5Y88

  • PubMed Abstract: 

    • The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an average resolution of 3.5 Å. The intron lariat remains bound in the spliceosome whereas the ligated exon is already dissociated ...

    The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an average resolution of 3.5 Å. The intron lariat remains bound in the spliceosome whereas the ligated exon is already dissociated. The step II splicing factors Prp17 and Prp18, along with Cwc21 and Cwc22 that stabilize the 5' exon binding to loop I of U5 small nuclear RNA (snRNA), have been released from the active site assembly. The DEAH family ATPase/helicase Prp43 binds Syf1 at the periphery of the spliceosome, with its RNA-binding site close to the 3' end of U6 snRNA. The C-terminal domain of Ntr1/Spp382 associates with the GTPase Snu114, and Ntr2 is anchored to Prp8 while interacting with the superhelical domain of Ntr1. These structural features suggest a plausible mechanism for the disassembly of the ILS complex.

    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: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114C1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114, GIN10, YKL173W, YKL637
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309G175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309, NTC25, YPR101W
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Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
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Pre-mRNA-splicing factor SYF1H859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1, NTC90, YDR416W
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1I687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1, NTC77, SYF3, YLR117C, L2952
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Entity ID: 10
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Pre-mRNA-splicing factor CEF1J590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1, NTC85, YMR213W, YM8261.07
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Entity ID: 11
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Pre-mRNA-splicing factor SYF2K215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2, NTC31, YGR129W
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Entity ID: 12
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Pre-mRNA-splicing factor BUD31L157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31, CWC14, YCR063W, YCR63W, YCR903
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Entity ID: 13
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Pre-mRNA-splicing factor SLT11M364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2, SLT11, YBR065C, YBR0614
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Entity ID: 14
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Pre-mRNA-splicing factor CWC2N339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2, NTC40, SLC3, YDL209C, D1041
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46O451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46, CWC1, NTC50, YPL151C, P2594
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Entity ID: 16
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Pre-mRNA-splicing factor CWC15P175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15, YDR163W, YD8358.17
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Entity ID: 17
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Pre-mRNA-processing protein 45Q379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45, FUN20, YAL032C
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Entity ID: 18
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Protein CWC16R278Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YJU2, CWC16, YKL095W, YKL442
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Entity ID: 19
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Pre-mRNA-processing factor 17S455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40, PRP17, SLU4, XRS2, YDR364C, D9481.11
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Entity ID: 20
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Pre-mRNA-splicing factor CWC23T283Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC23, YGL128C, G2861
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Entity ID: 21
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Pre-mRNA-splicing factor SPP382U708Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPP382, CCF8, NTR1, YLR424W
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Entity ID: 22
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Pre-mRNA-splicing factor NTR2V322Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NTR2, YKR022C
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Entity ID: 23
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Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43W767Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP43, YGL120C
EC: 3.6.4.13
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BX [auth a],
GA [auth h]		196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1, YER029C
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Entity ID: 25
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Small nuclear ribonucleoprotein EY [auth b],
HA [auth i]		94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1, YOR159C
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Entity ID: 26
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Small nuclear ribonucleoprotein FZ [auth c],
IA [auth j]		86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3, YPR182W, P9705.4
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Entity ID: 27
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Small nuclear ribonucleoprotein GAA [auth d],
JA [auth k]		77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2, SNP2, YFL017W-A, YFL017Bw
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Entity ID: 28
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Small nuclear ribonucleoprotein Sm D3BA [auth e],
KA [auth l]		101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3, YLR147C, L9634.6
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Entity ID: 29
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Small nuclear ribonucleoprotein Sm D1CA [auth f],
LA [auth m]		146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1, YGR074W
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Entity ID: 30
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Small nuclear ribonucleoprotein Sm D2DA [auth g],
MA [auth n]		110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2, YLR275W, L9328.5
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'EA [auth o]238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1, YPL213W
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Entity ID: 32
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U2 small nuclear ribonucleoprotein B''FA [auth p]111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1, YIR009W, YIB9W
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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: PRP19, PSO4, YLL036C
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
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U6 snRNAD 112Saccharomyces cerevisiae S288C
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Intron lariatE 38Saccharomyces cerevisiae S288C
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Entity ID: 6
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U2 snRNAF 1175Saccharomyces cerevisiae S288C
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Entity ID: 34
MoleculeChainsLengthOrganismImage
RNA (intron or U6 snRNA)RA [auth x]9Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
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SA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N		 Ligand Interaction
GTP
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TA [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 L],
DB [auth M],
EB [auth M],
AB [auth L],
BB [auth L],
CB [auth L],
DB [auth M],
EB [auth M],
FB [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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UA [auth C],
VA [auth D],
WA [auth D],
XA [auth D],
YA [auth D],
UA [auth C],
VA [auth D],
WA [auth D],
XA [auth D],
YA [auth D],
ZA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 2.0: 2020-10-14
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary