3AV1 Structural Protein Dna date Feb 18, 2011
title The Human Nucleosome Structure Containing The Histone Varian
authors H.Tachiwana, A.Osakabe, T.Shiga, Y.Miya, H.Kimura, W.Kagawa, H.Kur
compound source
Molecule: Histone H3.2
Chain: A, E
Synonym: Histone H3m, Histone H3o
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3.2
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 H2a.2, Histone H2aa, Histone H2am
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.1, Histone H2b.R, H2br
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
Other_details: The Dna Sequence Is Palindromic, Containing Halves A Human Alpha-Satellite Repeat.
symmetry Space Group: P 21 21 21
R_factor 0.244 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.466 109.628 181.930 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructures of human nucleosomes containing major histone H3 variants., Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H, Kagawa W, Kurumizaka H, Acta Crystallogr D Biol Crystallogr. 2011 Jun;67(Pt 6):578-83. Epub 2011 May 17. PMID:21636898
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (3av1.pdb1.gz) 241 Kb
  • CSU: Contacts of Structural Units for 3AV1
  • Structure Factors (620 Kb)
  • Retrieve 3AV1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AV1 from S2C, [Save to disk]
  • Re-refined 3av1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AV1 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 3AV1
  • 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 3AV1, from MSDmotif at EBI
  • Fold representative 3av1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3av1_D] [3av1_J] [3av1] [3av1_H] [3av1_G] [3av1_C] [3av1_E] [3av1_I] [3av1_A] [3av1_B] [3av1_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AV1: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3AV1
  • Community annotation for 3AV1 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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