7W59

The cryo-EM structure of human pre-C*-I complex


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 1.2 of the entry. See complete history


Literature

Mechanism of exon ligation by human spliceosome.

Zhan, X.Lu, Y.Zhang, X.Yan, C.Shi, Y.

(2022) Mol Cell 82: 2769-2778.e4

  • DOI: 10.1016/j.molcel.2022.05.021
  • Primary Citation of Related Structures:  
    7W59, 7W5A, 7W5B

  • PubMed Abstract: 
  • Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C -I and pre-C -II, both at 3 ...

    Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C -I and pre-C -II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C -I to pre-C -II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C -I, pre-C -II, and C complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C complexes, our studies recapitulate a molecular choreography of the C-to-C transition, revealing mechanistic insights into exon ligation.


    Organizational Affiliation

    Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. Electronic address: syg@westlake.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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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentB [auth C]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinC [auth E]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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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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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinG [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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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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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologI [auth N]144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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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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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologK [auth P]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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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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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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Entity ID: 14
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Pleiotropic regulator 1N [auth T]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2O [auth U]2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologP [auth V]908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17Q [auth W]579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'U [auth b],
LA [auth i]
240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
PSME3-interacting proteinV [auth X]254Homo sapiensMutation(s): 0 
Gene Names: PSME3IP1C16orf94FAM192ANIP30PIP30CDA018CDA10
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1W [auth I]855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EX [auth y]301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8Y1220Homo sapiensMutation(s): 0 
Gene Names: DHX8DDX8
EC: 3.6.4.13
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3Z [auth a],
KA [auth h]
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1AA [auth c],
MA [auth j]
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2BA [auth d],
NA [auth k]
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FCA [auth f],
OA [auth m]
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EDA [auth e],
PA [auth l]
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GEA [auth g],
QA [auth n]
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Protein mago nashi homologFA [auth v]146Homo sapiensMutation(s): 0 
Gene Names: MAGOHMAGOHA
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 8AGA [auth w]174Homo sapiensMutation(s): 0 
Gene Names: RBM8ARBM8HSPC114MDS014
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIHA [auth u]411Homo sapiensMutation(s): 0 
Gene Names: EIF4A3DDX48KIAA0111
EC: 3.6.4.13
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Protein CASC3IA [auth x]703Homo sapiensMutation(s): 0 
Gene Names: CASC3MLN51
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
RNA helicase aquariusJA [auth Q]1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'RA [auth o]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''SA [auth p]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19TA [auth q],
UA [auth r],
VA [auth s],
WA [auth t]
504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 2.3.2.27
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27XA [auth K]225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
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Entity ID: 4
MoleculeChainsLengthOrganismImage
pre-mRNAD [auth 4]46unidentified adenovirus
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Entity ID: 5
MoleculeChainsLengthOrganismImage
pre-mRNAE [auth G]174unidentified adenovirus
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Entity ID: 18
MoleculeChainsLengthOrganismImage
U5 snRNAR [auth B]117Homo sapiens
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Entity ID: 19
MoleculeChainsLengthOrganismImage
U6 snRNAS [auth F]107Homo sapiens
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Entity ID: 20
MoleculeChainsLengthOrganismImage
U2 snRNAT [auth H]188Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
YA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP

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ZA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP

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NB [auth Q]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

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BB [auth N],
CB [auth N],
DB [auth N],
EB [auth O],
FB [auth O],
BB [auth N],
CB [auth N],
DB [auth N],
EB [auth O],
FB [auth O],
GB [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

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AB [auth C],
HB [auth F],
IB [auth F],
JB [auth F],
KB [auth F],
AB [auth C],
HB [auth F],
IB [auth F],
JB [auth F],
KB [auth F],
LB [auth F],
MB [auth F],
OB [auth Q],
PB [auth Q]
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: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-11-29 
  • Released Date: 2022-06-22 
  • Deposition Author(s): Zhan, X., Lu, Y., Shi, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2022-08-17
    Changes: Database references