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 1.2 of the entry. See complete history. 


Literature

Structural insights into branch site proofreading by human spliceosome

Zhang, X., Zhan, X., Bian, T., Yang, F., Li, P., Lu, Y., Xing, Z., Fan, R., Zhang, Q.C., Shi, Y.

(2024) Nat Struct Mol Biol 


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1B [auth 1]1,304Homo sapiensMutation(s): 0 
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Find proteins for O75533 (Homo sapiens)
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PHAROS:  O75533
GTEx:  ENSG00000115524 
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UniProt GroupO75533
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2C [auth 2]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3D [auth 3]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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UniProt GroupQ15393
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4E [auth 4]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5F [auth 5]86Homo sapiensMutation(s): 0 
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PHAROS:  Q9BWJ5
GTEx:  ENSG00000169976 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AG [auth 6]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1H [auth A]793Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099995 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2I [auth B]464Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104897 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3J [auth C]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
HIV Tat-specific factor 1K [auth D]755Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102241 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicaseL [auth E]1,052Homo sapiensMutation(s): 0 
Gene Names: DDX46
EC: 3.6.4.13
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Find proteins for Q7L014 (Homo sapiens)
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GTEx:  ENSG00000145833 
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UniProt GroupQ7L014
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'M [auth F]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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UniProt GroupP09661
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''N [auth G]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2O [auth a]118Homo sapiensMutation(s): 0 
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Find proteins for P62316 (Homo sapiens)
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GTEx:  ENSG00000125743 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FP [auth b]86Homo sapiensMutation(s): 0 
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Find proteins for P62306 (Homo sapiens)
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GTEx:  ENSG00000139343 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EQ [auth c]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GR [auth d]76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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UniProt GroupP62308
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3S [auth e]126Homo sapiensMutation(s): 0 
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Find proteins for P62318 (Homo sapiens)
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GTEx:  ENSG00000100028 
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UniProt GroupP62318
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'T [auth f]240Homo sapiensMutation(s): 0 
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Find proteins for P14678 (Homo sapiens)
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GTEx:  ENSG00000125835 
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UniProt GroupP14678
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1U [auth g]119Homo sapiensMutation(s): 0 
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Find proteins for P62314 (Homo sapiens)
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GTEx:  ENSG00000167088 
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UniProt GroupP62314
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Entity ID: 1
MoleculeChains LengthOrganismImage
U2 snRNAA [auth H]188Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / 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
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
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



View more in-depth experimental data
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
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Database references