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 

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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: https://doi.org/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 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; Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 82,413Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU1141,008Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309175Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1859Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1687Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1590Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2215Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31157Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11364Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2339Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46451Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15175Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45379Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Protein CWC16278Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17455Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC23283Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPP382708Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor NTR2322Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43767Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BGA [auth h],
X [auth a]
196Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EHA [auth i],
Y [auth b]
94Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FIA [auth j],
Z [auth c]
86Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GAA [auth d],
JA [auth k]
77Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3BA [auth e],
KA [auth l]
101Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1CA [auth f],
LA [auth m]
146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2DA [auth g],
MA [auth n]
110Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'EA [auth o]238Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''FA [auth p]111Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19NA [auth q],
OA [auth r],
PA [auth s],
QA [auth t]
503Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.2.27
UniProt
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNA214Saccharomyces cerevisiae S288C
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Entity ID: 4
MoleculeChains LengthOrganismImage
U6 snRNA112Saccharomyces cerevisiae S288C
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Entity ID: 5
MoleculeChains LengthOrganismImage
Intron lariat38Saccharomyces cerevisiae S288C
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Entity ID: 6
MoleculeChains LengthOrganismImage
U2 snRNA1,175Saccharomyces cerevisiae S288C
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Entity ID: 34
MoleculeChains LengthOrganismImage
RNA (intron or U6 snRNA)RA [auth x]9Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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

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TA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
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
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

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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