4ZBJ Structural Protein date Apr 14, 2015
title Ubn1 Peptide Bound To H3.3h4asf1
authors R.Marmorstein, M.D.Ricketts, Y.Tang
compound source
Molecule: Histone Chaperone Asf1
Chain: A
Fragment: Unp Residues 2-169
Synonym: Anti-Silencing Function Protein 1,Yasf1
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Asf1, Cia1, Yjl115w, J0755
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_cell_line: Rosetta2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst39

Molecule: Histone H3
Chain: B
Fragment: Unp Residues 62-136
Engineered: Yes
Mutation: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_cell_line: Rosetta2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst39

Molecule: Histone H4
Chain: C
Fragment: Unp Residues 21-103
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_cell_line: Rosetta2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst39

Molecule: Ubinuclein-1
Chain: D
Fragment: Unp Residues 122-148
Synonym: Hira-Binding Protein,Protein Vt4,Ubiquitously Expr Nuclear Protein;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 32 2 1
R_factor 0.208 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.024 90.024 120.734 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.25 Å
ligand ACE, CL, MPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


Primary referenceUbinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex., Daniel Ricketts M, Frederick B, Hoff H, Tang Y, Schultz DC, Singh Rai T, Grazia Vizioli M, Adams PD, Marmorstein R, Nat Commun. 2015 Jul 10;6:7711. doi: 10.1038/ncomms8711. PMID:26159857
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (4zbj.pdb1.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 4ZBJ
  • CSU: Contacts of Structural Units for 4ZBJ
  • Structure Factors (269 Kb)
  • Retrieve 4ZBJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ZBJ from S2C, [Save to disk]
  • Re-refined 4zbj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ZBJ 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 4ZBJ
  • 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 4zbj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4zbj_A] [4zbj_D] [4zbj] [4zbj_B] [4zbj_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4ZBJ: [H3] [H4 ] by SMART
  • Other resources with information on 4ZBJ
  • Community annotation for 4ZBJ at PDBWiki (http://pdbwiki.org)

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