2CV5 Structural Protein Dna date May 31, 2005
title Crystal Structure Of Human Nucleosome Core Particle
authors Y.Tsunaka, N.Kajimura, S.Tate, K.Morikawa
compound source
Molecule: Dna (146-Mer)
Chain: I, J
Synonym: Palindromic 146-Bp Human A-Satellite Dna
Engineered: Yes
Synthetic: Yes

Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Histone H2a.A
Chain: C, G
Synonym: Histone H2a
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Histone H2b K
Chain: D, H
Synonym: Histone H2b, Hira-Interacting Protein 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 21 21 21
R_factor 0.224 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.564 108.370 169.425 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceAlteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle., Tsunaka Y, Kajimura N, Tate S, Morikawa K, Nucleic Acids Res 2005 Jun 10;33(10):3424-34. Print 2005. PMID:15951514
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (254 Kb) [Save to disk]
  • Biological Unit Coordinates (2cv5.pdb1.gz) 248 Kb
  • LPC: Ligand-Protein Contacts for 2CV5
  • CSU: Contacts of Structural Units for 2CV5
  • Likely Quarternary Molecular Structure file(s) for 2CV5
  • Structure Factors (519 Kb)
  • Retrieve 2CV5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2CV5 from S2C, [Save to disk]
  • Re-refined 2cv5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2CV5 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 2CV5
  • 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 2CV5, from MSDmotif at EBI
  • Fold representative 2cv5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2cv5_A] [2cv5_B] [2cv5_C] [2cv5_H] [2cv5] [2cv5_I] [2cv5_D] [2cv5_J] [2cv5_G] [2cv5_E] [2cv5_F]
  • SWISS-PROT database: [P04908] [O60814] [P68431] [P62805]
  • Domain organization of [H2A1B_HUMAN] [H2B1K_HUMAN] [H31_HUMAN] [H4_HUMAN] by SWISSPFAM
  • Domains found in 2CV5: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 2CV5
  • Community annotation for 2CV5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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