3AZM Structural Protein Dna date May 25, 2011
title Crystal Structure Of Human Nucleosome Core Particle Containi Mutation
authors W.Iwasaki, H.Tachiwana, K.Kawaguchi, T.Shibata, W.Kagawa, H.Kurum
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
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
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
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
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
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 0.241 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.792 108.767 174.515 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.89 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceComprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains., Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H, Biochemistry. 2011 Sep 13;50(36):7822-32. Epub 2011 Aug 17. PMID:21812398
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (248 Kb) [Save to disk]
  • Biological Unit Coordinates (3azm.pdb1.gz) 241 Kb
  • LPC: Ligand-Protein Contacts for 3AZM
  • CSU: Contacts of Structural Units for 3AZM
  • Structure Factors (385 Kb)
  • Retrieve 3AZM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AZM from S2C, [Save to disk]
  • Re-refined 3azm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AZM 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 3AZM
  • 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 3AZM, from MSDmotif at EBI
  • Fold representative 3azm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3azm_D] [3azm_A] [3azm_E] [3azm_I] [3azm_H] [3azm_C] [3azm_J] [3azm] [3azm_B] [3azm_F] [3azm_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AZM: [H2A] [H2B] [H3] [H4 ] by SMART
  • Alignments of the sequence of 3AZM with the sequences similar proteins can be viewed for 3AZM's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3AZM
  • Community annotation for 3AZM at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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