5XJT | pdb_00005xjt

Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1(1-82)/D2.R61A/F/E/G from Human

  • Classification: SPLICING
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2017-05-04 Released: 2018-07-04 
  • Deposition Author(s): Yi, H., Zhang, R.
  • Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 
    0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structures of 7S mutant complexes

Yi, H., Zhang, R.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gem-associated protein 2A [auth 2]280Homo sapiensMutation(s): 0 
Gene Names: GEMIN2, SIP1
UniProt & NIH Common Fund Data Resources
Find proteins for O14893 (Homo sapiens)
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PHAROS:  O14893
GTEx:  ENSG00000092208 
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UniProt GroupO14893
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1B [auth A]82Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens)
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PHAROS:  P62314
GTEx:  ENSG00000167088 
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UniProt GroupP62314
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2C [auth B]118Homo sapiensMutation(s): 1 
Gene Names: SNRPD2, SNRPD1
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PHAROS:  P62316
GTEx:  ENSG00000125743 
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UniProt GroupP62316
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ED [auth E]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Find proteins for P62304 (Homo sapiens)
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PHAROS:  P62304
GTEx:  ENSG00000182004 
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UniProt GroupP62304
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FE [auth F]86Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
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GTEx:  ENSG00000139343 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GF [auth G]76Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
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GTEx:  ENSG00000143977 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Survival motor neuron proteinG [auth M]37Homo sapiensMutation(s): 0 
Gene Names: SMN1, SMN, SMNT, SMN2, SMNC
UniProt & NIH Common Fund Data Resources
Find proteins for Q16637 (Homo sapiens)
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PHAROS:  Q16637
GTEx:  ENSG00000172062 ENSG00000205571 
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UniProt GroupQ16637
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.64α = 90
b = 84.76β = 90
c = 114.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570720
National Natural Science Foundation of ChinaChina81441109

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description