1F1E

CRYSTAL STRUCTURE OF THE HISTONE FROM METHANOPYRUS KANDLERI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An ancestral nuclear protein assembly: crystal structure of the Methanopyrus kandleri histone.

Fahrner, R.L.Cascio, D.Lake, J.A.Slesarev, A.

(2001) Protein Sci 10: 2002-2007

  • DOI: 10.1110/ps.10901
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Eukaryotic histone proteins condense DNA into compact structures called nucleosomes. Nucleosomes were viewed as a distinguishing feature of eukaryotes prior to identification of histone orthologs in methanogens. Although evolutionarily distinct from ...

    Eukaryotic histone proteins condense DNA into compact structures called nucleosomes. Nucleosomes were viewed as a distinguishing feature of eukaryotes prior to identification of histone orthologs in methanogens. Although evolutionarily distinct from methanogens, the methane-producing hyperthermophile Methanopyrus kandleri produces a novel, 154-residue histone (HMk). Amino acid sequence comparisons show that HMk differs from both methanogenic and eukaryotic histones, in that it contains two histone-fold ms within a single chain. The two HMk histone-fold ms, N and C terminal, are 28% identical in amino acid sequence to each other and approximately 21% identical in amino acid sequence to other histone proteins. Here we present the 1.37-A-resolution crystal structure of HMk and report that the HMk monomer structure is homologous to the eukaryotic histone heterodimers. In the crystal, HMk forms a dimer homologous to [H3-H4](2) in the eukaryotic nucleosome. Based on the spatial similarities to structural ms found in the eukaryotic nucleosome that are important for DNA-binding, we infer that the Methanopyrus histone binds DNA in a manner similar to the eukaryotic histone tetramer [H3-H4](2).


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1570, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE FOLD PROTEIN
A
154Methanopyrus kandleriMutation(s): 4 
Gene Names: hmk
Find proteins for O93641 (Methanopyrus kandleri)
Go to UniProtKB:  O93641
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.4α = 90
b = 57.4β = 90
c = 96.95γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description