6ID1

Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 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: 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 ...

    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

    School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang, 310024, China. shi-lab@tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8A2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentC972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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GTEx:  ENSG00000108883 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinD [auth E]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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GTEx:  ENSG00000060688 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1F [auth J]848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
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GTEx:  ENSG00000101343 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinG [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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GTEx:  ENSG00000096401 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2H [auth M]243Homo sapiensMutation(s): 0 
Gene Names: SYF2CBPINGCIPIP
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GTEx:  ENSG00000117614 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologI [auth N]144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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GTEx:  ENSG00000106245 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22J [auth O]420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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GTEx:  ENSG00000086589 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologK [auth P]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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GTEx:  ENSG00000150316 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1L [auth R]536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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GTEx:  ENSG00000100603 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1M [auth S]166Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1N [auth T]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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GTEx:  ENSG00000171566 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17O [auth W]579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
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GTEx:  ENSG00000168438 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
CWF19-like protein 2R [auth U]894Homo sapiensMutation(s): 0 
Gene Names: CWF19L2
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GTEx:  ENSG00000152404 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3S [auth a],
HA [auth h]
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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GTEx:  ENSG00000100028 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteinT [auth b],
IA [auth i]
231Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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GTEx:  ENSG00000125835 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1U [auth c],
JA [auth j]
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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GTEx:  ENSG00000167088 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2V [auth d],
KA [auth k]
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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GTEx:  ENSG00000125743 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FW [auth f],
LA [auth m]
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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GTEx:  ENSG00000139343 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EX [auth e],
MA [auth l]
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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GTEx:  ENSG00000182004 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GY [auth g],
NA [auth n]
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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GTEx:  ENSG00000143977 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19Z [auth q],
AA [auth r],
BA [auth s],
CA [auth t]
504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 2.3.2.27
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GTEx:  ENSG00000110107 
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Entity ID: 27
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Pre-mRNA-splicing factor SPF27DA [auth K]225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
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GTEx:  ENSG00000116752 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1EA [auth I]855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
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GTEx:  ENSG00000076924 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
RNA helicase aquariusFA [auth Q]1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EGA [auth y]301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
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GTEx:  ENSG00000084072 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'OA [auth o]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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GTEx:  ENSG00000131876 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''PA [auth p]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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GTEx:  ENSG00000125870 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15QA [auth V]795Homo sapiensMutation(s): 0 
Gene Names: DHX15DBP1DDX15
EC: 3.6.4.13
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GTEx:  ENSG00000109606 
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5snRNAB 117Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
U6snRNAE [auth F]107Homo sapiens
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Entity ID: 16
MoleculeChainsLengthOrganismImage
pre-mRNAP [auth G]272Homo sapiens
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Entity ID: 17
MoleculeChainsLengthOrganismImage
U2snRNAQ [auth H]188Homo sapiens
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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 N],
BB [auth N],
CB [auth N],
DB [auth O],
EB [auth O],
AB [auth N],
BB [auth N],
CB [auth N],
DB [auth O],
EB [auth O],
FB [auth O],
GB [auth U]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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TA [auth C],
UA [auth F],
VA [auth F],
WA [auth F],
XA [auth F],
TA [auth C],
UA [auth F],
VA [auth F],
WA [auth F],
XA [auth F],
YA [auth F],
ZA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
L [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 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