1P3F Structural Protein Dna date Apr 17, 2003
title Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'Sin' Mutants
authors U.M.Muthurajan, Y.Bao, L.J.Forsberg, R.S.Edayathumangalam, P.N.Dyer, C.L.White, K.Luger
compound source
Molecule: Palindromic 146bp Human Alpha-Satellite Dna Fragment;
Chain: I, J
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Hb 101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.739 109.499 181.649 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
related structures by homologous chain: 1P3A, 1P3K
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceCrystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions., Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K, EMBO J 2004 Jan 28;23(2):260-71. Epub 2004 Jan 22. PMID:14739929
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (230 Kb) [Save to disk]
  • Biological Unit Coordinates (1p3f.pdb1.gz) 221 Kb
  • CSU: Contacts of Structural Units for 1P3F
  • Likely Quarternary Molecular Structure file(s) for 1P3F
  • Retrieve 1P3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1P3F from S2C, [Save to disk]
  • View 1P3F 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 1P3F
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1P3F, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1p3fa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1p3fb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1p3fc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1p3fd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1p3fe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1p3ff_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1p3fg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1p3fh_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1p3f 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: [1p3f_A] [1p3f_D] [1p3f] [1p3f_I] [1p3f_F] [1p3f_H] [1p3f_C] [1p3f_J] [1p3f_E] [1p3f_B] [1p3f_G]
  • SWISS-PROT database: [P06897] [P02281] [P84233] [P62799]
  • Domain organization of [H2A1_XENLA] [H2B11_XENLA] [H32_XENLA] [H4_XENLA] by SWISSPFAM
  • Domains found in 1P3F: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 1P3F
  • Community annotation for 1P3F 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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