4BRY | pdb_00004bry

The Idas:Geminin heterodimeric parallel coiled-coil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.226 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4BRY

This is version 1.3 of the entry. See complete history

Literature

The Geminin and Idas Coiled Coils Preferentially Form a Heterodimer that Inhibits Geminin Function in DNA Replication Licensing

Caillate, C.Pefani, E.D.Gillespie, P.J.Taraviras, S.Blow, J.J.Lygerou, Z.Perrakis, A.

(2013) J Biological Chem 288: 31624

  • DOI: https://doi.org/10.1074/jbc.M113.491928
  • Primary Citation Related Structures: 
    4BRY

  • PubMed Abstract: 

    Geminin is an important regulator of proliferation and differentiation in metazoans, which predominantly inhibits the DNA replication licensing factor Cdt1, preventing genome over-replication. We show that Geminin preferentially forms stable coiled-coil heterodimers with its homologue, Idas. In contrast to Idas-Geminin heterodimers, Idas homodimers are thermodynamically unstable and are unlikely to exist as a stable macromolecule under physiological conditions. The crystal structure of the homology regions of Idas in complex with Geminin showed a tight head-to-head heterodimeric coiled-coil. This Idas-Geminin heterodimer binds Cdt1 less strongly than Geminin-Geminin, still with high affinity (∼30 nm), but with notably different thermodynamic properties. Consistently, in Xenopus egg extracts, Idas-Geminin is less active in licensing inhibition compared with a Geminin-Geminin homodimer. In human cultured cells, ectopic expression of Idas leads to limited over-replication, which is counteracted by Geminin co-expression. The properties of the Idas-Geminin complex suggest it as the functional form of Idas and provide a possible mechanism to modulate Geminin activity.


  • Organizational Affiliation
    • From the Division of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 18.34 kDa 
  • Atom Count: 1,175 
  • Modeled Residue Count: 138 
  • Deposited Residue Count: 151 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GEMININ78Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75496 (Homo sapiens)
Explore O75496 
Go to UniProtKB:  O75496
PHAROS:  O75496
GTEx:  ENSG00000112312 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75496
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MULTICILIN73Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for D6RGH6 (Homo sapiens)
Explore D6RGH6 
Go to UniProtKB:  D6RGH6
PHAROS:  D6RGH6
GTEx:  ENSG00000234602 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6RGH6
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.226 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.799α = 90
b = 117.799β = 90
c = 103.462γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description