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 Diffraction	resolution	2.50 Å
ligand	CL, MN	enzyme
Gene Ontology	Chain Function Process Component A, E C, G F, B H, D
Primary reference	Structural 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] (246 Kb) [Save to disk] Biological Unit Coordinates (3afa.pdb1.gz) 240 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

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 3D motif for 3AFA, from MSDmotif at EBI

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)

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