5KGF Structural Protein Dna date Jun 13, 2016
title Structural Model Of 53bp1 Bound To A Ubiquitylated And Methy Nucleosome, At 4.5 A Resolution
authors M.D.Wilson, S.Benlekbir, F.Sicheri, J.L.Rubinstein, D.Durocher
compound source
Molecule: Histone H3.2
Chain: A, E
Synonym: Histone H3
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Synonym: Histone H4kc20me2
Engineered: Yes
Mutation: Yes
Other_details: Cysteine Alkylation At Position 20

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1
Chain: C, G
Synonym: H2a.1, Histone H2ap
Engineered: Yes
Mutation: Yes
Other_details: Isopeptide Amide Crosslink Between K15 Of H2 Of Ubiquitin;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ag, H2afp, Hist1h2ai, H2afc, Hist1h2ak, H2afd, Hist1h2al, H2afi, Hist1h2am, H2afn;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-Cefgi
Chain: D, H
Synonym: Histone H2b.1 A, Histone H2b.A, H2ba, Histone H2b Histone H2b.H, H2bh, Histone H2b.K, H2bk, Histone H2b.L,
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bc, H2bfl, Hist1h2be, H2bfh, Hist1h2bf, H2bfg, Hist1h2bg, H2bfa, Hist1h2bi, H2bfk;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (145-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tumor Suppressor P53-Binding Protein 1
Chain: L, K
Engineered: Yes
Other_details: Full Protein Not Modeled

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tp53bp1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin
Chain: O, M
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.54 Å
ligand M2L enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceThe structural basis of modified nucleosome recognition by 53BP1., Wilson MD, Benlekbir S, Fradet-Turcotte A, Sherker A, Julien JP, McEwan A, Noordermeer SM, Sicheri F, Rubinstein JL, Durocher D, Nature. 2016 Aug 4;536(7614):100-3. PMID:27462807
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (279 Kb) [Save to disk]
  • Biological Unit Coordinates (5kgf.pdb1.gz) 271 Kb
  • LPC: Ligand-Protein Contacts for 5KGF
  • CSU: Contacts of Structural Units for 5KGF
  • Retrieve 5KGF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KGF from S2C, [Save to disk]
  • View 5KGF 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 5KGF
  • 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
  • Fold representative 5kgf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kgf_J] [5kgf_L] [5kgf_B] [5kgf_H] [5kgf_K] [5kgf_M] [5kgf_I] [5kgf_O] [5kgf_A] [5kgf_E] [5kgf_F] [5kgf_D] [5kgf_C] [5kgf] [5kgf_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5KGF: [H2A] [H2B] [H3] [H4] [UBQ ] by SMART
  • Other resources with information on 5KGF
  • Community annotation for 5KGF at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science