6CIM Recombination Dna date Feb 24, 2018
title Pre-Reaction Complex, Rag1(E962q)2-Nickedintact 1223rss C Mn2+
authors W.Chuenchor, X.Chen, M.S.Kim, M.Gellert, W.Yang
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
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rag1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293t
Expression_system_plasmid: Plexm

Molecule: V(D)J Recombination-Activating Protein 2
Chain: B, D
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
Expression_system_cell_line: Hek293t
Expression_system_plasmid: Plexm

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
Cell_line: H
Gene: Hmgb1, Hmg1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Nicked 12rss Intermediate Reverse Strand
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpcpcptpgptpcptptpa)-3')
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Nicked 12rss Intermediate Forward Strand
Chain: L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Intact 23rss Substrate Reverse Strand
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Intact 23rss Substrate Forward Strand
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.214 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
156.678 123.562 186.286 90.00 105.60 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand MN, ZN enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


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] (393 Kb) [Save to disk]
  • Biological Unit Coordinates (6cim.pdb1.gz) 383 Kb
  • LPC: Ligand-Protein Contacts for 6CIM
  • CSU: Contacts of Structural Units for 6CIM
  • Structure Factors (1110 Kb)
  • Retrieve 6CIM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CIM from S2C, [Save to disk]
  • View 6CIM 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 6CIM
  • 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 6cim from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6cim_C] [6cim_I] [6cim_B] [6cim_G] [6cim_A] [6cim_D] [6cim_F] [6cim_L] [6cim_J] [6cim_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6CIM
  • Community annotation for 6CIM 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