6ID0

Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Structures of the human spliceosomes before and after release of the ligated exon.

Zhang, X.Zhan, X.Yan, C.Zhang, W.Liu, D.Lei, J.Shi, Y.

(2019) Cell Res 29: 274-285

  • DOI: https://doi.org/10.1038/s41422-019-0143-x
  • Primary Citation of Related Structures:  
    6ICZ, 6ID0, 6ID1

  • PubMed Abstract: 

    Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3'-splice site is recognized by the junction between the 5'-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly.


  • 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. shi-lab@tsinghua.edu.cn.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,335Homo sapiensMutation(s): 0 
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PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein component972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinD [auth E]357Homo sapiensMutation(s): 0 
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PHAROS:  Q96DI7
GTEx:  ENSG00000060688 
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UniProt GroupQ96DI7
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1F [auth J]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinG [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2H [auth M]243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologI [auth N]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22J [auth O]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologK [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1L [auth R]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1M [auth S]166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1N [auth T]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17O [auth W]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
CWF19-like protein 2R [auth U]894Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000152404 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1S [auth I]855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3FA [auth h],
T [auth a]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteinGA [auth i],
U [auth b]
231Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1HA [auth j],
V [auth c]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2IA [auth k],
W [auth d]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FJA [auth m],
X [auth f]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EKA [auth l],
Y [auth e]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GLA [auth n],
Z [auth g]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19AA [auth q],
BA [auth r],
CA [auth s],
DA [auth t]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000110107 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27EA [auth K]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'MA [auth o]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''NA [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicase aquariusOA [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EPA [auth y]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000084072 
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5snRNA117Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
U6snRNAE [auth F]107Homo sapiens
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Entity ID: 16
MoleculeChains LengthOrganismImage
pre-mRNAP [auth G]272Homo sapiens
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Entity ID: 17
MoleculeChains LengthOrganismImage
U2snRNAQ [auth H]188Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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

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

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AB [auth N]
BB [auth N]
CB [auth O]
DB [auth O]
EB [auth O]
AB [auth N],
BB [auth N],
CB [auth O],
DB [auth O],
EB [auth O],
FB [auth U],
ZA [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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SA [auth C]
TA [auth F]
UA [auth F]
VA [auth F]
WA [auth F]
SA [auth C],
TA [auth F],
UA [auth F],
VA [auth F],
WA [auth F],
XA [auth F],
YA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
L [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 2.0: 2020-10-14
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary