PDBsum entry 1hta

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Histone PDB id
Protein chain
68 a.a. *
Waters ×56
* Residue conservation analysis
PDB id:
Name: Histone
Title: Crystal structure of the histone hmfa from methanothermus fe
Structure: Histone hmfa. Chain: a. Engineered: yes
Source: Methanothermus fervidus. Organism_taxid: 2180. Gene: hmfa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.55Å     R-factor:   0.200     R-free:   0.248
Authors: K.Decanniere,K.Sandman,J.N.Reeve,U.Heinemann
Key ref:
K.Decanniere et al. (2000). Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus. J Mol Biol, 303, 35-47. PubMed id: 11021968 DOI: 10.1006/jmbi.2000.4104
18-Mar-98     Release date:   23-Mar-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P48781  (HMFA_METFE) -  DNA-binding protein HMf-1
69 a.a.
68 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   3 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1006/jmbi.2000.4104 J Mol Biol 303:35-47 (2000)
PubMed id: 11021968  
Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus.
K.Decanniere, A.M.Babu, K.Sandman, J.N.Reeve, U.Heinemann.
The hyperthermophilic archaeon Methanothermus fervidus contains two small basic proteins, HMfA (68 amino acid residues) and HMfB (69 residues) that share a common ancestry with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. HMfA and HMfB have sequences that differ at 11 locations, they have different structural stabilities, and the complexes that they form with DNA have different electrophoretic mobilities. Here, crystal structures are documented for recombinant (r) HMfA at a resolution of 1.55 A refined to a crystallographic R-value of 19.8 % (tetragonal form) and at 1.48 A refined to a R-value of 18.8 % (orthorhombic form), and for rHMfB at 1.9 A refined to a R-value of 18.0 %. The rHMfA and rHMfB monomers have structures that are just histone folds in which a long central alpha-helix (alpha2; 29 residues) is separated from shorter N-terminal (alpha1; 11 residues) and C-terminal (alpha3; 10 residues) alpha-helices by two loops (L1 and L2; both 6 residues). Within L1 and L2, three adjacent residues are in extended (beta) conformation. rHMfA and rHMfB assemble into homodimers, with the alpha2 helices anti-parallel aligned and crossing at an angle of close to 35 degrees, and with hydrogen bonds formed between the extended, parallel regions of L1 and L2 resulting in short beta-ladders. Dimerization creates a novel N-terminal structure that contains four proline residues, two from each monomer. As prolines are present at these positions in all archaeal histone sequences, this proline-tetrad structure is likely to be a common feature of all archaeal histone dimers. Almost all residues that participate in monomer-monomer interactions are conserved in HMfA and HMfB, consistent with the ability of these monomers to form both homodimers and (HMfA+HMfB) heterodimers. Differences in side-chain interactions that result from non-conservative residue differences in HMfA and HMfB are identified, and the structure of a (rHMfA)(2)-DNA complex is presented based on the structures documented here and modeled by homology to histone-DNA interactions in the eukaryal nucleosome.
  Selected figure(s)  
Figure 2.
Figure 2. Crystal structure of (rHMfA)[2] and comparison with (rHMfB)[2]. (a) Schematic drawing of (rHMfA)[2] identifying the α-helical and loop regions of the histone fold. The molecule is color-coded to show structural similarity with (rHMfB)[2]. Based on the least-squares superposition of the dimers, the α-carbon positions deviate at most by ≤1.4 Å, in the areas indicated by red. (b) Stereographic drawing of the (HMfA)[2] crystal structure with the protein backbone drawn using heavier lines than used for the side-chains.
Figure 6.
Figure 6. Model for DNA binding by (rHMfA)[2]. The model was generated by (rHMfA)[2] replacement of a (H3+H4) dimer in the eukaryal nucleosome crystal structure [Luger et al 1997] as described in the text. The L1-L2a and paired N-terminal regions predicted to contact the DNA are boxed (A and B, respectively), and shown in expanded format in Figure 7.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 35-47) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265758 R.P.Driessen, and R.T.Dame (2011).
Nucleoid-associated proteins in Crenarchaea.
  Biochem Soc Trans, 39, 116-121.  
20140026 S.C.Dillon, and C.J.Dorman (2010).
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression.
  Nat Rev Microbiol, 8, 185-195.  
20351259 S.P.Wilkinson, M.Ouhammouch, and E.P.Geiduschek (2010).
Transcriptional activation in the context of repression mediated by archaeal histones.
  Proc Natl Acad Sci U S A, 107, 6777-6781.  
19047349 U.Friedrich-Jahn, J.Aigner, G.Längst, J.N.Reeve, and H.Huber (2009).
Nanoarchaeal origin of histone H3?
  J Bacteriol, 191, 1092-1096.  
18515342 A.Mukherjee, A.O.Sokunbi, and A.Grove (2008).
DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima.
  Nucleic Acids Res, 36, 3956-3968.  
18096639 M.R.Stump, and L.M.Gloss (2008).
Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate.
  Protein Sci, 17, 322-332.  
18976667 M.R.Stump, and L.M.Gloss (2008).
Mutational analysis of the stability of the H2A and H2B histone monomers.
  J Mol Biol, 384, 1369-1383.  
16920388 K.Sandman, and J.N.Reeve (2006).
Archaeal histones and the origin of the histone fold.
  Curr Opin Microbiol, 9, 520-525.  
16287087 Y.Qiu, V.Tereshko, Y.Kim, R.Zhang, F.Collart, M.Yousef, A.Kossiakoff, and A.Joachimiak (2006).
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
  Proteins, 62, 8.
PDB code: 1r4v
16242031 B.D.Silverman (2005).
Asymmetry in the burial of hydrophobic residues along the histone chains of eukarya, archaea and a transcription factor.
  BMC Struct Biol, 5, 20.  
15871046 B.D.Silverman (2005).
The hydrophobicity of the H3 histone fold differs from the hydrophobicity of the other three folds.
  J Mol Evol, 60, 354-364.  
15856481 J.Roach, S.Sharma, M.Kapustina, and C.W.Carter (2005).
Structure alignment via Delaunay tetrahedralization.
  Proteins, 60, 66-81.  
16030242 L.Cubonová, K.Sandman, S.J.Hallam, E.F.Delong, and J.N.Reeve (2005).
Histones in crenarchaea.
  J Bacteriol, 187, 5482-5485.  
16094450 M.S.Cosgrove, and C.Wolberger (2005).
How does the histone code work?
  Biochem Cell Biol, 83, 468-476.  
15096635 D.D.Banks, and L.M.Gloss (2004).
Folding mechanism of the (H3-H4)2 histone tetramer of the core nucleosome.
  Protein Sci, 13, 1304-1316.  
15150236 Y.Xie, and J.N.Reeve (2004).
Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome.
  J Bacteriol, 186, 3492-3498.  
12754245 D.J.Soares, F.Marc, and J.N.Reeve (2003).
Conserved eukaryotic histone-fold residues substituted into an archaeal histone increase DNA affinity but reduce complex flexibility.
  J Bacteriol, 185, 3453-3457.  
14627741 G.Wang, R.Guo, M.Bartlam, H.Yang, H.Xue, Y.Liu, L.Huang, and Z.Rao (2003).
Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii.
  Protein Sci, 12, 2815-2822.
PDB code: 1nh9
14583738 H.S.Malik, and S.Henikoff (2003).
Phylogenomics of the nucleosome.
  Nat Struct Biol, 10, 882-891.  
12694606 J.N.Reeve (2003).
Archaeal chromatin and transcription.
  Mol Microbiol, 48, 587-598.  
12058041 F.Marc, K.Sandman, R.Lurz, and J.N.Reeve (2002).
Archaeal histone tetramerization determines DNA affinity and the direction of DNA supercoiling.
  J Biol Chem, 277, 30879-30886.  
12077456 G.Wang, R.Guo, M.Bartlam, H.Xue, H.Yang, Y.Liu, L.Huang, and Z.Rao (2002).
Expression, purification, crystallization and preliminary X-ray analysis of a DNA-binding protein from Methanococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 58, 1240-1242.  
12093751 J.M.Hadden, A.C.Déclais, S.E.Phillips, and D.M.Lilley (2002).
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.
  EMBO J, 21, 3505-3515.
PDB codes: 1m0d 1m0i
11751933 K.A.Bailey, F.Marc, K.Sandman, and J.N.Reeve (2002).
Both DNA and histone fold sequences contribute to archaeal nucleosome stability.
  J Biol Chem, 277, 9293-9301.  
12446147 M.F.White, and S.D.Bell (2002).
Holding it together: chromatin in the Archaea.
  Trends Genet, 18, 621-626.  
11976507 T.Li, X.Ji, F.Sun, R.Gao, S.Cao, Y.Feng, and Z.Rao (2002).
Crystallization and preliminary X-ray analysis of recombinant histone HPhA from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Acta Crystallogr D Biol Crystallogr, 58, 870-871.  
11278079 K.Sandman, D.Soares, and J.N.Reeve (2001).
Molecular components of the archaeal nucleosome.
  Biochimie, 83, 277-281.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.