3X1U Structural Protein Dna date Nov 28, 2014
title Crystal Structure Of Nucleosome Core Particle In The Presenc Histone Variants 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
Chain: C, G
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: H2aa
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-B
Chain: D, H
Synonym: Histone H2b.1, Histone H2b.F, H2bf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2b
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 0.200 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.427 109.184 175.001 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.25 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] (250 Kb) [Save to disk]
  • Biological Unit Coordinates (3x1u.pdb1.gz) 243 Kb
  • LPC: Ligand-Protein Contacts for 3X1U
  • CSU: Contacts of Structural Units for 3X1U
  • Structure Factors (383 Kb)
  • Retrieve 3X1U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3X1U from S2C, [Save to disk]
  • Re-refined 3x1u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3X1U 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 3X1U
  • 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 3x1u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3x1u_B] [3x1u_H] [3x1u_C] [3x1u_A] [3x1u] [3x1u_D] [3x1u_E] [3x1u_G] [3x1u_I] [3x1u_J] [3x1u_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3X1U: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3X1U
  • Community annotation for 3X1U at PDBWiki (http://pdbwiki.org)

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