2E9X

The crystal structure of human GINS core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the human GINS complex and its assembly and functional interface in replication initiation

Kamada, K.Kubota, Y.Arata, T.Shindo, Y.Hanaoka, F.

(2007) Nat Struct Mol Biol 14: 388-396

  • DOI: https://doi.org/10.1038/nsmb1231
  • Primary Citation of Related Structures:  
    2E9X

  • PubMed Abstract: 

    The eukaryotic GINS complex is essential for the establishment of DNA replication forks and replisome progression. We report the crystal structure of the human GINS complex. The heterotetrameric complex adopts a pseudo symmetrical layered structure comprising two heterodimers, creating four subunit-subunit interfaces. The subunit structures of the heterodimers consist of two alternating domains. The C-terminal domains of the Sld5 and Psf1 subunits are connected by linker regions to the core complex, and the C-terminal domain of Sld5 is important for core complex assembly. In contrast, the C-terminal domain of Psf1 does not contribute to the stability of the complex but is crucial for chromatin binding and replication activity. These data suggest that the core complex ensures a stable platform for the C-terminal domain of Psf1 to act as a key interaction interface for other proteins in the replication-initiation process.


  • Organizational Affiliation

    Cellular Physiology Laboratory, RIKEN Discovery Research Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. kamadak@riken.jp


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1
A, E
149Homo sapiensMutation(s): 0 
Gene Names: PSF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14691 (Homo sapiens)
Explore Q14691 
Go to UniProtKB:  Q14691
PHAROS:  Q14691
GTEx:  ENSG00000101003 
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UniProt GroupQ14691
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2
B, F
185Homo sapiensMutation(s): 0 
Gene Names: PSF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y248 (Homo sapiens)
Explore Q9Y248 
Go to UniProtKB:  Q9Y248
PHAROS:  Q9Y248
GTEx:  ENSG00000131153 
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UniProt GroupQ9Y248
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GINS complex subunit 3
C, G
219Homo sapiensMutation(s): 0 
Gene Names: psf3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRX5 (Homo sapiens)
Explore Q9BRX5 
Go to UniProtKB:  Q9BRX5
PHAROS:  Q9BRX5
GTEx:  ENSG00000181938 
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UniProt GroupQ9BRX5
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
GINS complex subunit 4
D, H
223Homo sapiensMutation(s): 0 
Gene Names: sld5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRT9 (Homo sapiens)
Explore Q9BRT9 
Go to UniProtKB:  Q9BRT9
PHAROS:  Q9BRT9
GTEx:  ENSG00000147536 
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UniProt GroupQ9BRT9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.928α = 104.689
b = 88.741β = 102.964
c = 102.129γ = 95.467
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations