4R7Z

PfMCM-AAA double-octamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.301 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.7554/eLife.03433
  • Primary Citation of Related Structures:  
    4R7Y, 4R7Z

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 21
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
338Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: MCMPF0482
UniProt
Find proteins for Q8U3I4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3I4 
Go to UniProtKB:  Q8U3I4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U3I4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
IA [auth J]
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
IA [auth J],
KA [auth K],
MA [auth L],
OA [auth M],
Q [auth A],
QA [auth N],
S [auth B],
SA [auth O],
U [auth C],
UA [auth P],
W [auth D],
Y [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth G]
FA [auth H]
HA [auth I]
JA [auth J]
BA [auth F],
DA [auth G],
FA [auth H],
HA [auth I],
JA [auth J],
LA [auth K],
NA [auth L],
PA [auth M],
R [auth A],
RA [auth N],
T [auth B],
TA [auth O],
V [auth C],
VA [auth P],
X [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.301 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.956α = 71.85
b = 127.082β = 72.82
c = 128.025γ = 80.39
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Database references
  • Version 1.3: 2014-11-19
    Changes: Database references
  • Version 1.4: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description