5IY0

PfMCM N-terminal domain double hexamer

• PDB DOI: https://doi.org/10.2210/pdb5IY0/pdb

• Classification: REPLICATION DNA BINDING PROTEIN
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-23 Released: 2016-07-13 
• Deposition Author(s): Meagher, M., Enemark, E.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Structure of a double hexamer of the Pyrococcus furiosus minichromosome maintenance protein N-terminal domain.

Meagher, M., Enemark, E.J.

(2016) Acta Crystallogr F Struct Biol Commun 72: 545-551

• PubMed: 27380371 
• DOI: https://doi.org/10.1107/S2053230X1600858X
• Primary Citation of Related Structures:  
  5IY0


• PubMed Abstract: 
  

  The crystal structure of the N-terminal domain of the Pyrococcus furiosus minichromosome maintenance (MCM) protein as a double hexamer is described. The MCM complex is a ring-shaped helicase that unwinds DNA at the replication fork of eukaryotes and archaea. Prior to replication initiation, the MCM complex assembles as an inactive double hexamer at specific sites of DNA. The presented structure is highly consistent with previous MCM double-hexamer structures and shows two MCM hexamers with a head-to-head interaction mediated by the N-terminal domain. Minor differences include a diminished head-to-head interaction and a slightly reduced inter-hexamer rotation.

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Organizational Affiliation: 

Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 176.8 kDa 
• Atom Count: 12,192 
• Modelled Residue Count: 1,518 
• Deposited Residue Count: 1,542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 21	A, B, C, D, E, F	257	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0482 EC: 3.6.4.12
UniProt
Find proteins for Q8U3I4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3I4  Go to UniProtKB:  Q8U3I4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.427	α = 90
b = 122.61	β = 92.35
c = 111.892	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-13 
Deposition Author(s): Meagher, M., Enemark, E.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM098771

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2016-07-20
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description