3AFA Structural Protein Dna date Feb 24, 2010
title The Human Nucleosome Structure
authors H.Tachiwana, W.Kagawa, A.Osakabe, K.Koichiro, T.Shiga, H.Kimura, H.Kurumizaka
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a, Histone H3b, Histone H3c, Histone Histone H3f, Histone H3h, Histone H3i, Histone H3j, His Histone H3l;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2a Type 1-Be
Chain: C, G
Synonym: Histone H2am, Histone H2aa, Histone H2a.2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: Histone H2b Type 1-J
Chain: D, H
Synonym: Histone H2b.R, H2br, Histone H2b.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: 146-Mer Dna
Chain: I, J
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.240 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.839 109.509 180.919 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T., Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H, Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10454-9. Epub 2010 May 24. PMID:20498094
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (250 Kb) [Save to disk]
  • Biological Unit Coordinates (3afa.pdb1.gz) 244 Kb
  • LPC: Ligand-Protein Contacts for 3AFA
  • CSU: Contacts of Structural Units for 3AFA
  • Structure Factors (631 Kb)
  • Retrieve 3AFA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AFA from S2C, [Save to disk]
  • Re-refined 3afa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AFA in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3AFA
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3AFA, from MSDmotif at EBI
  • Fold representative 3afa from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3afa_J] [3afa_E] [3afa_G] [3afa] [3afa_H] [3afa_A] [3afa_F] [3afa_D] [3afa_I] [3afa_B] [3afa_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AFA: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3AFA
  • Community annotation for 3AFA at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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