7EVO

The cryo-EM structure of the human 17S U2 snRNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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

Structural Mechanisms of the RNA Helicases DDX42 and PRP5 in Pre-spliceosome Assembly

Zhang, X.Zhan, X.Yang, F.Bian, T.Lu, Y.Shi, Y.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1B [auth 1]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2C [auth 2]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3D [auth 3]1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4E [auth 4]424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5F [auth 5]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AG [auth 6]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1H [auth A]793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2I [auth B]464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3J [auth C]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
HIV Tat-specific factor 1K [auth D]755Homo sapiensMutation(s): 0 
Gene Names: HTATSF1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
RNA helicaseL [auth E]1052Homo sapiensMutation(s): 0 
Gene Names: DDX46
EC: 3.6.4.13
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'M [auth F]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''N [auth G]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2O [auth a]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FP [auth b]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EQ [auth c]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GR [auth d]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3S [auth e]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'T [auth f]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1U [auth g]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U2 snRNAA [auth H]188Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9B0 (Subject of Investigation/LOI)
Query on 9B0

Download Ideal Coordinates CCD File 
V [auth 1][(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate
C40 H66 N2 O9
MNOMBFWMICHMKG-MGYWSNOQSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
W [auth 6],
X [auth 6],
Y [auth 6],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release