4ME3

1.8 Angstrom Crystal Structure of the N-terminal Domain of an Archaeal MCM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.3 of the entry. See complete history


Literature

The 1.8- angstrom Crystal Structure of the N-Terminal Domain of an Archaeal MCM as a Right-Handed Filament.

Fu, Y.Slaymaker, I.M.Wang, J.Wang, G.Chen, X.S.

(2014) J Mol Biol 426: 1512-1523

  • DOI: https://doi.org/10.1016/j.jmb.2013.12.025
  • Primary Citation of Related Structures:  
    4ME3

  • PubMed Abstract: 

    Mini-chromosome maintenance (MCM) proteins are the replicative helicase necessary for DNA replication in both eukarya and archaea. Most of archaea only have one MCM gene. Here, we report a 1.8-Å crystal structure of the N-terminal MCM from the archaeon Thermoplasma acidophilum (tapMCM). In the structure, the MCM N-terminus forms a right-handed filament that contains six subunits in each turn, with a diameter of 25Å of the central channel opening. The inner surface is highly positively charged, indicating DNA binding. This filament structure with six subunits per turn may also suggests a potential role for an open-ring structure for hexameric MCM and dynamic conformational changes in initiation and elongation stages of DNA replication.


  • Organizational Affiliation

    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: Xiaojiang.chen@usc.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM related protein268Thermoplasma acidophilumMutation(s): 0 
Gene Names: Ta0799
UniProt
Find proteins for Q9HK10 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HK10 
Go to UniProtKB:  Q9HK10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HK10
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.46α = 90
b = 93.46β = 90
c = 56.231γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references
  • Version 1.2: 2014-03-26
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description