6ZFF

Pyrococcus furiosus Rad50 coiled coils in rod configuration


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A rod conformation of the Pyrococcus furiosus Rad50 coiled coil.

Soh, Y.M.Basquin, J.Gruber, S.

(2021) Proteins 89: 251-255

  • DOI: https://doi.org/10.1002/prot.26005
  • Primary Citation of Related Structures:  
    6ZFF

  • PubMed Abstract: 

    The Rad50-Mre11 nuclease complex plays a vital role in DNA repair in all domains of life. It recognizes and processes DNA double-strand breaks. Rad50 proteins fold into an extended structure with a 20 to 60 nm long coiled coil connecting a globular ABC ATPase domain with a zinc hook dimerization domain. A published structure of an archaeal Rad50 zinc hook shows coiled coils pointing away from each other. Here we present the crystal structure of an alternate conformation displaying co-aligned coiled coils. Archaeal Rad50 may thus switch between rod-shaped and ring-like conformations as recently proposed for a bacterial homolog.


  • Organizational Affiliation

    Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA double-strand break repair Rad50 ATPase
A, B
140Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rad50PF1167
UniProt
Find proteins for P58301 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore P58301 
Go to UniProtKB:  P58301
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58301
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 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.3α = 90
b = 128.3β = 90
c = 74.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)ERC COG 724482
National Research Foundation (NRF, Korea)Korea, Republic Of2017R1A6A3A03006597

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references, Derived calculations
  • Version 1.2: 2021-01-20
    Changes: Database references