6CIJ Recombination Dna date Feb 24, 2018
title Cryo-Em Structure Of Mouse Rag12 Hfc Complex Containing Par Linker(3.9 A)
authors X.Chen, M.Kim, W.Chuenchor, Y.Cui, X.Zhang, Z.H.Zhou, M.Gellert, W.
compound source
Molecule: V(D)J Recombination-Activating Protein 1
Chain: A, C
Synonym: Rag-1
Ec: 3.1.-.-,2.3.2.27
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rag1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Dna (46-Mer)
Chain: F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpaptpcptpgpgpcpcptpgptpcp 3');
Chain: I
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'- D(Pcptpgpgpaptpcptpgpgpcpcptpgptpcptptpa
Chain: J
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (60-Mer)
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: High Mobility Group Protein B1
Chain: N
Synonym: High Mobility Group Protein 1,Hmg-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hmgb1, Hmg1
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333

Molecule: Dna (30-Mer)
Chain: L
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: V(D)J Recombination-Activating Protein 2
Chain: D, B
Synonym: Rag-2
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rag2, Rag-2
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Dna (41-Mer)
Chain: M
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
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 3.90 Å
ligand CA, ZN enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B
  • methylated histone binding
  • ubiquitin protein ligase act...


    • N


    Primary referenceCracking the DNA Code for V(D)J Recombination., Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W, Mol Cell. 2018 Apr 19;70(2):358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Epub, 2018 Apr 5. PMID:29628308
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (370 Kb) [Save to disk]
  • Biological Unit Coordinates (6cij.pdb1.gz) 362 Kb
  • LPC: Ligand-Protein Contacts for 6CIJ
  • CSU: Contacts of Structural Units for 6CIJ
  • Retrieve 6CIJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CIJ from S2C, [Save to disk]
    • View 6CIJ 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 6CIJ
  • 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: [6cij_C] [6cij_D] [6cij_F] [6cij_I] [6cij_M] [6cij_A] [6cij_N] [6cij_B] [6cij_G] [6cij_J] [6cij_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6CIJ
  • Community annotation for 6CIJ at PDBWiki (http://pdbwiki.org)

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