1ID3 Structural Protein Dna date Apr 03, 2001
title Crystal Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Differences In Inter-Nucleosome Interactions
authors C.L.White, R.K.Suto, K.Luger
compound source
Molecule: Palindromic 146bp Dna Fragment
Chain: I, J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Alpha Sat Dna
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Histone H3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Histone H4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Histone H2a.1
Chain: C, G
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Histone H2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Histone H2b.2
Chain: D, H
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Histone H2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.292
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.922 110.398 192.617 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions., White CL, Suto RK, Luger K, EMBO J 2001 Sep 17;20(18):5207-18. PMID:11566884
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (227 Kb) [Save to disk]
  • Biological Unit Coordinates (1id3.pdb1.gz) 220 Kb
  • LPC: Ligand-Protein Contacts for 1ID3
  • CSU: Contacts of Structural Units for 1ID3
  • Likely Quarternary Molecular Structure file(s) for 1ID3
  • Structure Factors (302 Kb)
  • Retrieve 1ID3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ID3 from S2C, [Save to disk]
  • Re-refined 1id3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1ID3 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 1ID3
  • 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 1ID3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1id3a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1id3b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1id3c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1id3d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1id3e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1id3f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1id3g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1id3h_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1id3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1id3_E] [1id3_H] [1id3_G] [1id3_B] [1id3] [1id3_F] [1id3_D] [1id3_J] [1id3_A] [1id3_C] [1id3_I]
  • SWISS-PROT database: [P04911] [P02294] [P61830] [P02309]
  • Domain organization of [H2A1_YEAST] [H2B2_YEAST] [H3_YEAST] [H4_YEAST] by SWISSPFAM
  • Domains found in 1ID3: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 1ID3
  • Community annotation for 1ID3 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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