7W5A

The cryo-EM structure of human pre-C*-II 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 1.0 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 


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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentC972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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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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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1I855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1J848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27K225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2M243Homo sapiensMutation(s): 0 
Gene Names: SYF2CBPINGCIPIP
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologN144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22O420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologP229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
RNA helicase aquariusQ1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1R536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1S166Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1T514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2U2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologV908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17W579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
PSME3-interacting proteinX254Homo sapiensMutation(s): 0 
Gene Names: PSME3IP1C16orf94FAM192ANIP30PIP30CDA018CDA10
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Find proteins for Q9GZU8 (Homo sapiens)
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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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Find proteins for Q14562 (Homo sapiens)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
CactinZ758Homo sapiensMutation(s): 0 
Gene Names: CACTINC19orf29
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Find proteins for Q8WUQ7 (Homo sapiens)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
PRKR-interacting protein 1AA [auth 2]184Homo sapiensMutation(s): 0 
Gene Names: PRKRIP1
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FAM32ABA [auth z]112Homo sapiensMutation(s): 0 
Gene Names: FAM32AOTAG12CGI-144
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'CA [auth b],
TA [auth i]
240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Find proteins for P14678 (Homo sapiens)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EDA [auth y]301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3EA [auth a],
SA [auth h]
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1FA [auth c],
UA [auth j]
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2GA [auth d],
VA [auth k]
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FHA [auth f],
WA [auth m]
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EIA [auth e],
XA [auth l]
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GJA [auth g],
YA [auth n]
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Protein mago nashi homologKA [auth v]146Homo sapiensMutation(s): 0 
Gene Names: MAGOHMAGOHA
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 8ALA [auth w]174Homo sapiensMutation(s): 0 
Gene Names: RBM8ARBM8HSPC114MDS014
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIIMA [auth u]411Homo sapiensMutation(s): 0 
Gene Names: EIF4A3DDX48KIAA0111
EC: 3.6.4.13
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Find proteins for P38919 (Homo sapiens)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Protein CASC3NA [auth x]703Homo sapiensMutation(s): 0 
Gene Names: CASC3MLN51
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19OA [auth q],
PA [auth r],
QA [auth s],
RA [auth t]
504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 2.3.2.27
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'ZA [auth o]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''AB [auth p]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7BB [auth 1]586Homo sapiensMutation(s): 0 
Gene Names: SLU7
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Find proteins for O95391 (Homo sapiens)
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB 117Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
U6 snRNAE [auth F]107Homo sapiens
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Entity ID: 6
MoleculeChainsLengthOrganismImage
Pre-mRNAF [auth 4]46unidentified adenovirus
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Entity ID: 7
MoleculeChainsLengthOrganismImage
Pre-mRNAG 174unidentified adenovirus
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Entity ID: 8
MoleculeChainsLengthOrganismImage
U2 snRNAH 188Homo sapiens
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

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

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

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

Download Ideal Coordinates CCD File 
LB [auth N],
MB [auth N],
NB [auth N],
OB [auth O],
PB [auth O],
LB [auth N],
MB [auth N],
NB [auth N],
OB [auth O],
PB [auth O],
QB [auth O],
UB [auth 1]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
EB [auth C],
FB [auth F],
GB [auth F],
HB [auth F],
IB [auth F],
EB [auth C],
FB [auth F],
GB [auth F],
HB [auth F],
IB [auth F],
JB [auth F],
KB [auth F],
SB [auth Q],
TB [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
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