5AV8 Dna Binding Protein Dna date Jun 12, 2015
title Human Nucleosome Core Particle
authors M.Wakamori, Y.Fujii, T.Umehara, S.Yokoyama
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a,Histone H3b,Histone H3c,Histone H3 H3f,Histone H3h,Histone H3i,Histone H3j,Histone H3k,Hi H3l;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h3a, H3fa, Hist1h3b, H3fl, Hist1h3c, H3fc, Hist1 H3fb, Hist1h3e, H3fd, Hist1h3f, H3fi, Hist1h3g, H3fh, Hist1 H3fk, Hist1h3i, H3ff, Hist1h3j, H3fj;
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a, H4a, H4fa, Hist1h4b, H4i, H4fi, Hist1h4c, H4fg, Hist1h4d, H4b, H4fb, Hist1h4e, H4j, H4fj, Hist1h4f, H4fc, Hist1h4h, H4h, H4fh, Hist1h4i, H4m, H4fm, Hist1h4j, H4fe, Hist1h4k, H4d, H4fd, Hist1h4l, H4k, H4fk, Hist2h4a, H4f2, H4fn, Hist2h4, Hist2h4b, H4o, H4fo, Hist4h4;
Expression_system: Cell-Free Synthesis
Other_details: Escherichia Coli

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: Hist1h2ab, H2afm, Hist1h2ae, H2afa
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

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: Hist1h2bj, H2bfr
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.191 109.955 181.887 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceIntra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation., Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S, Sci Rep. 2015 Nov 26;5:17204. doi: 10.1038/srep17204. PMID:26607036
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (259 Kb) [Save to disk]
  • Biological Unit Coordinates (5av8.pdb1.gz) 252 Kb
  • LPC: Ligand-Protein Contacts for 5AV8
  • CSU: Contacts of Structural Units for 5AV8
  • Structure Factors (600 Kb)
  • Retrieve 5AV8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5AV8 from S2C, [Save to disk]
  • Re-refined 5av8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5AV8 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 5AV8
  • 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
  • Fold representative 5av8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5av8_A] [5av8] [5av8_J] [5av8_I] [5av8_H] [5av8_E] [5av8_D] [5av8_F] [5av8_G] [5av8_C] [5av8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5AV8: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 5AV8
  • Community annotation for 5AV8 at PDBWiki (http://pdbwiki.org)

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