3AZL	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 0.208 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 106.580 109.636 182.213 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	CL, MN	enzyme
Gene Ontology	Chain Function Process Component A, E DNA binding protein binding protein heterodimerization a... nucleosome assembly blood coagulation S phase regulation of gene silencing... nucleosome extracellular region nucleus nucleoplasm chromosome C, G DNA binding protein heterodimerization a... nucleosome assembly nucleosome nucleus chromosome F, B DNA binding protein binding protein heterodimerization a... telomere maintenance chromatin organization nucleosome assembly CENP-A containing nucleosome... negative regulation of megak... phosphatidylinositol-mediate... nucleosome extracellular region nucleus nucleoplasm chromosome nucleolus actin cytoskeleton H, D DNA binding nucleosome assembly defense response to bacteriu... nucleosome nucleus chromosome
Primary reference	Comprehensive 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] (252 Kb) [Save to disk] Biological Unit Coordinates (3azl.pdb1.gz) 245 Kb LPC: Ligand-Protein Contacts for 3AZL CSU: Contacts of Structural Units for 3AZL Structure Factors (496 Kb) Retrieve 3AZL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3AZL from S2C, [Save to disk] Re-refined 3azl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3AZL 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3AZL

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 3AZL, from MSDmotif at EBI Fold representative 3azl from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3azl_A] [3azl_B] [3azl_C] [3azl_D] [3azl_E] [3azl_F] [3azl_G] [3azl_H] [3azl_I] [3azl_J] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3AZL with the sequences similar proteins can be viewed for 3AZL'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 3AZL

Community annotation for 3AZL at PDBWiki (http://pdbwiki.org)

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