PDBsum entry 3afa

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protein dna_rna metals Protein-protein interface(s) links
Structural protein/DNA PDB id
Protein chains
97 a.a. *
78 a.a. *
108 a.a. *
96 a.a. *
84 a.a. *
_CL ×4
_MN ×8
Waters ×183
* Residue conservation analysis
PDB id:
Name: Structural protein/DNA
Title: The human nucleosome structure
Structure: Histone h3.1. Chain: a, e. Synonym: histone h3/a, histone h3/b, histone h3/c, histone histone h3/f, histone h3/h, histone h3/i, histone h3/j, his histone h3/l. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: h3.1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: h4. Gene: h2a. Gene: h2b.
2.50Å     R-factor:   0.240     R-free:   0.270
Authors: H.Tachiwana,W.Kagawa,A.Osakabe,K.Koichiro,T.Shiga,H.Kimura, H.Kurumizaka
Key ref: H.Tachiwana et al. (2010). Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc Natl Acad Sci U S A, 107, 10454-10459. PubMed id: 20498094
24-Feb-10     Release date:   26-May-10    
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Protein chains
Pfam   ArchSchema ?
P68431  (H31_HUMAN) -  Histone H3.1
136 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P62805  (H4_HUMAN) -  Histone H4
103 a.a.
78 a.a.
Protein chains
Pfam   ArchSchema ?
P04908  (H2A1B_HUMAN) -  Histone H2A type 1-B/E
130 a.a.
108 a.a.
Protein chains
Pfam   ArchSchema ?
P06899  (H2B1J_HUMAN) -  Histone H2B type 1-J
126 a.a.
96 a.a.
Protein chain
Pfam   ArchSchema ?
P62805  (H4_HUMAN) -  Histone H4
103 a.a.
84 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   10 terms 
  Biological process     regulation of gene silencing   17 terms 
  Biochemical function     histone demethylase activity (H4-K20 specific)     5 terms  


Proc Natl Acad Sci U S A 107:10454-10459 (2010)
PubMed id: 20498094  
Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T.
H.Tachiwana, W.Kagawa, A.Osakabe, K.Kawaguchi, T.Shiga, Y.Hayashi-Takanaka, H.Kimura, H.Kurumizaka.
A histone H3 variant, H3T, is highly expressed in the testis, suggesting that it may play an important role in the chromatin reorganization required for meiosis and/or spermatogenesis. In the present study, we found that the nucleosome containing human H3T is significantly unstable both in vitro and in vivo, as compared to the conventional nucleosome containing H3.1. The crystal structure of the H3T nucleosome revealed structural differences in the H3T regions on both ends of the central alpha2 helix, as compared to those of H3.1. The H3T-specific residues (Met71 and Val111) are the source of the structural differences observed between H3T and H3.1. A mutational analysis revealed that these residues are responsible for the reduced stability of the H3T-containing nucleosome. These physical and structural properties of the H3T-containing nucleosome may provide the basis of chromatin reorganization during spermatogenesis.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21743476 H.Tachiwana, W.Kagawa, T.Shiga, A.Osakabe, Y.Miya, K.Saito, Y.Hayashi-Takanaka, T.Oda, M.Sato, S.Y.Park, H.Kimura, and H.Kurumizaka (2011).
Crystal structure of the human centromeric nucleosome containing CENP-A.
  Nature, 476, 232-235.
PDB code: 3an2
21173468 T.Gruene, and G.M.Sheldrick (2011).
Geometric properties of nucleic acids with potential for autobuilding.
  Acta Crystallogr A, 67, 1-8.  
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