1E69 | pdb_00001e69

SMC head domain from Thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.272 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1E69

This is version 1.5 of the entry. See complete history

Literature

Crystal Structure of the Smc Head Domain: An Abc ATPase with 900 Residues Antiparallel Coiled-Coil Inserted

Lowe, J.Cordell, S.C.van den Ent, F.

(2001) J Mol Biology 306: 25

  • DOI: https://doi.org/10.1006/jmbi.2000.4379
  • Primary Citation Related Structures: 
    1E69

  • PubMed Abstract: 

    SMC (structural maintenance of chromosomes) proteins are large coiled-coil proteins involved in chromosome condensation, sister chromatid cohesion, and DNA double-strand break processing. They share a conserved five-domain architecture with three globular domains separated by two long coiled-coil segments. The coiled-coil segments are antiparallel, bringing the N and C-terminal globular domains together. We have expressed a fusion protein of the N and C-terminal globular domains of Thermotoga maritima SMC in Escherichia coli by replacing the approximately 900 residue coiled-coil and hinge segment with a short peptide linker. The SMC head domain (SMChd) binds and condenses DNA in an ATP-dependent manner. Using selenomethionine-substituted protein and multiple anomalous dispersion phasing, we have solved the crystal structure of the SMChd to 3.1 A resolution. In the monoclinic crystal form, six SMChd molecules form two turns of a helix. The fold of SMChd is closely related to the ATP-binding cassette (ABC) ATPase family of proteins and Rad50, a member of the SMC family involved in DNA double-strand break repair. In SMChd, the ABC ATPase fold is formed by the N and C-terminal domains with the 900 residue coiled-coil and hinge segment inserted in the middle of the fold. The crystal structure of an SMChd confirms that the coiled-coil segments in SMC proteins are anti-parallel and shows how the N and C-terminal domains come together to form an ABC ATPase. Comparison to the structure of the MukB N-terminal domain demonstrates the close relationship between MukB and SMC proteins, and indicates a helix to strand conversion when N and C-terminal parts come together.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK. jyl@mrc-lmb.cam.ac.uk

Macromolecule Content 

  • Total Structure Weight: 215.35 kDa 
  • Atom Count: 12,396 
  • Modeled Residue Count: 1,578 
  • Deposited Residue Count: 1,932 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CHROMOSOME SEGREGATION SMC PROTEIN
A, B, C, D, E
A, B, C, D, E, F
322Thermotoga maritimaMutation(s): 0 
UniProt
Find proteins for Q9X0R4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0R4 
Go to UniProtKB:  Q9X0R4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0R4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.272 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134α = 90
b = 49.19β = 94.63
c = 233.88γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
SnBphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Database references, Source and taxonomy
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Other