4R7Y

Crystal structure of an active MCM hexamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Analysis of the crystal structure of an active MCM hexamer.

Miller, J.M.Arachea, B.T.Epling, L.B.Enemark, E.J.

(2014) Elife 3: e03433-e03433

  • DOI: 10.7554/eLife.03433
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a n ...

    In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis.


    Organizational Affiliation

    Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Minichromosome maintenance protein MCM, Cell division control protein 21
A, B
613Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
This entity is chimeric
Mutation(s): 0 
Gene Names: MCM,
EC: 3.6.4.12
Find proteins for Q9UXG1 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q9UXG1
Find proteins for Q8U3I4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U3I4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.263 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 118.902α = 90.00
b = 118.902β = 90.00
c = 199.317γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Database references
  • Version 1.3: 2014-11-19
    Type: Database references
  • Version 1.4: 2017-08-02
    Type: Refinement description, Source and taxonomy