7DPD

Human MCM9 N-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural study of the N-terminal domain of human MCM8/9 complex.

Li, J.Yu, D.Liu, L.Liang, H.Ouyang, Q.Liu, Y.

(2021) Structure 29: 1171-1181.e4

  • DOI: https://doi.org/10.1016/j.str.2021.05.006
  • Primary Citation of Related Structures:  
    7DP3, 7DPD

  • PubMed Abstract: 

    MCM8/9 is a complex involved in homologous recombination (HR) repair pathway. MCM8/9 dysfunction can cause genome instability and result in primary ovarian insufficiency (POI). However, the mechanism underlying these effects is largely unknown. Here, we report crystal structures of the N-terminal domains (NTDs) of MCM8 and MCM9, and build a ring-shaped NTD structure based on a 6.6 Å resolution cryoelectron microscopy map. This shows that the MCM8/9 complex forms a 3:3 heterohexamer in an alternating pattern. A positively charged DNA binding channel and a putative ssDNA exit pathway for fork DNA unwinding are revealed. Based on the atomic model, the potential effects of the clinical POI mutants are interpreted. Surprisingly, the zinc-finger motifs are found to be capable of binding an iron atom as well. Overall, our results provide a model for the formation of the MCM8/9 complex and provide a path for further studies.


  • Organizational Affiliation

    School of Medicine, Sun Yat-Sen University, Guangdong 510006, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA helicase MCM9
A, B
291Homo sapiensMutation(s): 2 
Gene Names: MCM9C6orf61MCMDC1
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXL9 (Homo sapiens)
Explore Q9NXL9 
Go to UniProtKB:  Q9NXL9
PHAROS:  Q9NXL9
GTEx:  ENSG00000111877 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXL9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.286α = 90
b = 85.9β = 90
c = 111.511γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2021-06-09
    Changes: Database references
  • Version 1.3: 2021-10-27
    Changes: Database references
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description