2PYO Structural Protein Dna date May 16, 2007
title Drosophila Nucleosome Core
authors C.R.Clapier, C.Petosa, C.W.Mueller
compound source
Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H3
Chain: A, E
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His3
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His4, H4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His2a, H2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b
Chain: D, H
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: His2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.030 182.040 109.420 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.43 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer., Clapier CR, Chakravarthy S, Petosa C, Fernandez-Tornero C, Luger K, Muller CW, Proteins. 2007 Oct 23;. PMID:17957772
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (2pyo.pdb1.gz) 245 Kb
  • LPC: Ligand-Protein Contacts for 2PYO
  • CSU: Contacts of Structural Units for 2PYO
  • Likely Quarternary Molecular Structure file(s) for 2PYO
  • Structure Factors (695 Kb)
  • Retrieve 2PYO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PYO from S2C, [Save to disk]
  • Re-refined 2pyo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PYO 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 2PYO
  • 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 2PYO, from MSDmotif at EBI
  • Fold representative 2pyo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pyo_A] [2pyo_D] [2pyo_E] [2pyo_H] [2pyo_B] [2pyo_J] [2pyo_F] [2pyo] [2pyo_C] [2pyo_I] [2pyo_G]
  • SWISS-PROT database: [P84051] [P02283] [P02299] [P84040]
  • Domain organization of [H2A_DROME] [H2B_DROME] [H3_DROME] [H4_DROME] by SWISSPFAM
  • Domains found in 2PYO: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 2PYO
  • Community annotation for 2PYO 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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