6USJ Dna Binding Protein Dna date Oct 27, 2019
title Structure Of Two Nucleosomes Bridged By Human Parp2
authors G.Gaullier, S.Bowerman, K.Luger
compound source
Molecule: Widom 601 Dna (160-Mer)
Chain: I, S
Engineered: Yes
Other_details: Widom 601 Nucleosome Positioning Sequence Wi 11 Additional Terminal Base Pairs;
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Widom 601 Dna (160-Mer)
Chain: J, T
Engineered: Yes

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

Molecule: Histone H3.1
Chain: A, E, K, O
Synonym: Histone H3a,Histone H3b,Histone H3c,Histone H3 H3f,Histone H3h,Histone H3i,Histone H3j,Histone H3k,Hi H3l;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3c1, H3fa, Hist1h3a, H3c2, H3fl, Hist1h3b, H3c3, H3f Hist1h3c, H3c4, H3fb, Hist1h3d, H3c6, H3fd, Hist1h3e, H3c7, Hist1h3f, H3c8, H3fh, Hist1h3g, H3c10, H3fk, Hist1h3h, H3c1 Hist1h3i, H3c12, H3fj, Hist1h3j;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H4c1, H4a, H4fa, Hist1h4a, H4c2, H4i, H4fi, Hist1h4 H4g, H4fg, Hist1h4c, H4c4, H4b, H4fb, Hist1h4d, H4c5, H4 Hist1h4e, H4c6, H4c, H4fc, Hist1h4f, H4c8, H4h, H4fh, His H4c9, H4m, H4fm, Hist1h4i, H4c11, H4e, H4fe, Hist1h4j, H4 H4d, H4fd, Hist1h4k, H4c13, H4k, H4fk, Hist1h4l, H4c14, H H4f2, H4fn, Hist2h4, Hist2h4a, H4c15, H4o, H4fo, Hist2h4b, Hist4h4;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ab, Hist1h2ae, Hcg_1640984, Hcg_1787383
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-J
Chain: D, H, N, R
Synonym: Histone H2b.1,Histone H2b.R,H2br
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj, H2bfr
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Poly [Adp-Ribose] Polymerase 2
Chain: U, V
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
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Variant: Isoform 2
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 10.50 Å
ligand
enzyme Transferase E.C.2.4.2.30 BRENDA
Primary referenceBridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1., Gaullier G, Roberts G, Muthurajan UM, Bowerman S, Rudolph J, Mahadevan J, Jha A, Rae PS, Luger K, PLoS One. 2020 Nov 3;15(11):e0240932. doi: 10.1371/journal.pone.0240932., eCollection 2020. PMID:33141820
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (493 Kb) [Save to disk]
  • Biological Unit Coordinates (6usj.pdb1.gz) 474 Kb
  • CSU: Contacts of Structural Units for 6USJ
  • Retrieve 6USJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6USJ from S2C, [Save to disk]
  • View 6USJ 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 6USJ
  • 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 6usj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6usj_S] [6usj_M] [6usj_A] [6usj_C] [6usj_E] [6usj_J] [6usj_P] [6usj_I] [6usj_L] [6usj_V] [6usj_D] [6usj_U] [6usj_T] [6usj_F] [6usj_N] [6usj_K] [6usj_R] [6usj_Q] [6usj_O] [6usj_G] [6usj_B] [6usj_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6USJ
  • Community annotation for 6USJ at PDBWiki (http://pdbwiki.org)

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