3X1V Structural Protein Dna date Nov 28, 2014
title Crystal Structure Of Nucleosome Core Particle In The Presenc Histone Variant Involved In Reprogramming
authors P.Sivaraman, T.S.Kumarevel
compound source
Molecule: Dna (146-Mer)
Chain: I, J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic
Organism_taxid: 32630

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
Gene: H3.1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: Histone H2b Type 1-A
Chain: D, H
Synonym: Histone H2b, Testis, Testis-Specific Histone H2b
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: H2ba
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.327 108.471 168.677 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.92 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming., Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T, Biochem Biophys Res Commun. 2015 Aug 28;464(3):929-35. doi:, 10.1016/j.bbrc.2015.07.070. Epub 2015 Jul 17. PMID:26188507
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (3x1v.pdb1.gz) 240 Kb
  • LPC: Ligand-Protein Contacts for 3X1V
  • CSU: Contacts of Structural Units for 3X1V
  • Structure Factors (381 Kb)
  • Retrieve 3X1V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3X1V from S2C, [Save to disk]
  • Re-refined 3x1v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3X1V 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 3X1V
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3x1v_B] [3x1v_J] [3x1v_H] [3x1v_F] [3x1v_C] [3x1v_A] [3x1v] [3x1v_E] [3x1v_D] [3x1v_G] [3x1v_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3X1V: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3X1V
  • Community annotation for 3X1V at PDBWiki (http://pdbwiki.org)

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