6ERH Dna Binding Protein date Oct 18, 2017
title Complex Of Xlf And Heterodimer Ku Bound To Dna
authors C.Nemoz, P.Legrand, V.Ropars, J.B.Charbonnier
compound source
Molecule: X-Ray Repair Cross-Complementing Protein 6
Chain: A, C
Synonym: 5'-Deoxyribose-5-Phosphate Lyase Ku70,5'-Drp Lyase Kda Subunit Of Ku Antigen,Atp-Dependent Dna Helicase 2 Subu Dependent Dna Helicase II 70 Kda Subunit,Ctc Box-Binding Fa Kda Subunit,Ctcbf,Dna Repair Protein Xrcc6,Lupus Ku Autoant Protein P70,Ku70,Thyroid-Lupus Autoantigen,Tlaa,X-Ray Repai Complementing Defective Repair In Chinese Hamster Cells 6;
Ec: 3.6.4.-,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Xrcc6, G22p1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector_type: Baculovirus

Molecule: X-Ray Repair Cross-Complementing Protein 5
Chain: B, D
Synonym: 86 Kda Subunit Of Ku Antigen,Atp-Dependent Dna Hel Subunit 2,Atp-Dependent Dna Helicase II 80 Kda Subunit,Ctc Binding Factor 85 Kda Subunit,Ctcbf,Dna Repair Protein Xrcc Ku86,Lupus Ku Autoantigen Protein P86,Nuclear Factor Iv,Thy Autoantigen,Tlaa,X-Ray Repair Complementing Defective Repai Chinese Hamster Cells 5 (Double-Strand-Break Rejoining);
Ec: 3.6.4.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Xrcc5, G22p2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector: Unidentified Baculovirus

Molecule: Dna (34-Mer)
Chain: F, O
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (21-Mer)
Chain: K, R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Non-Homologous End-Joining Factor 1
Chain: M, T
Synonym: Protein Cernunnos,Xrcc4-Like Factor
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.225 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.847 118.925 128.219 90.00 93.11 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand SO4 enzyme Hydrolase E.C.3.6.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceXLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining., Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB, Nat Struct Mol Biol. 2018 Oct;25(10):971-980. doi: 10.1038/s41594-018-0133-6., Epub 2018 Oct 5. PMID:30291363
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (814 Kb) [Save to disk]
  • Biological Unit Coordinates (6erh.pdb1.gz) 408 Kb
  • Biological Unit Coordinates (6erh.pdb2.gz) 404 Kb
  • LPC: Ligand-Protein Contacts for 6ERH
  • CSU: Contacts of Structural Units for 6ERH
  • Structure Factors (2258 Kb)
  • Retrieve 6ERH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ERH from S2C, [Save to disk]
  • View 6ERH 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 6ERH
  • 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 6erh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6erh_A] [6erh_D] [6erh_T] [6erh_F] [6erh_R] [6erh_B] [6erh_K] [6erh_C] [6erh_M] [6erh_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6ERH
  • Community annotation for 6ERH at PDBWiki (http://pdbwiki.org)

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