OCA Atlas for 3AZJ

3AZJ

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

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

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

Synthetic: Yes

symmetry

Space Group: P 21 21 21

R_factor

0.220

R_Free

0.268

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
105.955	109.428	180.904	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.89 Å

ligand

CL, MN

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, E
C, G
F, B
H, D

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] (245 Kb) [Save to disk]

Biological Unit Coordinates (3azj.pdb1.gz) 238 Kb

LPC: Ligand-Protein Contacts for 3AZJ

CSU: Contacts of Structural Units for 3AZJ

Structure Factors (409 Kb)

Retrieve 3AZJ in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3AZJ from S2C, [Save to disk]

Re-refined 3azj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3AZJ 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 3AZJ

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 3AZJ, from MSDmotif at EBI

Fold representative 3azj from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3azj_I] [3azj_C] [3azj_J] [3azj_G] [3azj_B] [3azj_D] [3azj_H] [3azj_E] [3azj_F] [3azj_A] [3azj]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3AZJ: [H2A] [H2B] [H3] [H4 ] by SMART

Other resources with information on 3AZJ

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

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]