6X0N Gene Regulation date May 16, 2020
title Bridging Of Double-Strand Dna Break Activates Parp2hpf1 To Chromatin
authors M.Halic, S.Bilokapic
compound source
Molecule: Histone H3.2
Chain: A, E, a, e
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, b, f
Engineered: Yes

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

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, H2ac14, Loc494591, Xelaev_18003602mg
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D, H, d, h
Synonym: H2b1.1
Engineered: Yes

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

Molecule: Dna (167-Mer)
Chain: I, I
Engineered: Yes

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

Molecule: Dna (167-Mer)
Chain: J, j
Engineered: Yes

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

Molecule: Histone Parylation Factor 1
Chain: O
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hpf1, C4orf27
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Poly [Adp-Ribose] Polymerase 2
Chain: P, R
Synonym: Hparp-2,Adp-Ribosyltransferase Diphtheria Toxin-Li Artd2,Dna Adp-Ribosyltransferase Parp2,Nad(+) Adp-Ribosyltr 2,Adprt-2,Poly[Adp-Ribose] Synthase 2,Padprt-2,Protein Poly Ribosyltransferase Parp2;
Ec: 2.4.2.30,2.4.2.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Parp2, Adprt2, Adprtl2
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 10.00 Å
ligand
enzyme Transferase E.C.2.4.2.30 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, f, B, b


O


P, R


a, E, A, e


d, h, H, D


g, C, c, G


Primary referenceBridging of DNA breaks activates PARP2-HPF1 to modify chromatin., Bilokapic S, Suskiewicz MJ, Ahel I, Halic M, Nature. 2020 Sep;585(7826):609-613. doi: 10.1038/s41586-020-2725-7. Epub 2020 Sep, 16. PMID:32939087
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (546 Kb) [Save to disk]
  • Biological Unit Coordinates (6x0n.pdb1.gz) 536 Kb
  • CSU: Contacts of Structural Units for 6X0N
  • Retrieve 6X0N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6X0N from S2C, [Save to disk]
  • View 6X0N 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 6X0N
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6x0n_h] [6x0n_g] [6x0n_G] [6x0n_A] [6x0n_P] [6x0n_a] [6x0n_I] [6x0n_O] [6x0n_b] [6x0n_C] [6x0n_e] [6x0n_F] [6x0n_f] [6x0n_i] [6x0n_J] [6x0n_B] [6x0n_c] [6x0n_E] [6x0n_d] [6x0n_D] [6x0n_j] [6x0n_H] [6x0n_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6X0N
  • Community annotation for 6X0N at PDBWiki (http://pdbwiki.org)

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