Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 17.25 kDa 
• Atom Count: 1415 
• Modelled Residue Count: 151 
• Deposited Residue Count: 154 
• Unique protein chains: 1

1F1E

CRYSTAL STRUCTURE OF THE HISTONE FROM METHANOPYRUS KANDLERI

• PDB DOI: 10.2210/pdb1F1E/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Methanopyrus kandleri
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-05-18 Released: 2001-10-31 
• Deposition Author(s): Fahrner, R.L., Cascio, D., Lake, J.A., Slesarev, A.

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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 

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

• PubMed: 11567091 
• DOI: 10.1110/ps.10901
• Primary Citation of Related Structures:  
  1F1E


• 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 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).

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE FOLD PROTEIN	A	154	Methanopyrus kandleri	Mutation(s): 4  Gene Names: hmk
UniProt
Find proteins for O93641 (Methanopyrus kandleri) Explore O93641  Go to UniProtKB:  O93641

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 57.4	α = 90
b = 57.4	β = 90
c = 96.95	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-18 
• Released Date: 2001-10-31 
Deposition Author(s): Fahrner, R.L., Cascio, D., Lake, J.A., Slesarev, A.

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