› 6cim

X-ray diffraction
3.6Å resolution

Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+

Released:
DOI: 10.2210/pdb6cim/pdb
PDB entry 6cim coloured by chain, front view.
PDB entry 6cim coloured by chain, side view.
PDB entry 6cim coloured by chain, top view.
Source organisms:
Primary publication:
Cracking 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 70 358-370.e4 (2018)
PMID: 29628308

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-119668 (preferred)
Entry contents:
3 distinct polypeptide molecules
5 distinct DNA molecules
Macromolecules (8 distinct):
V(D)J recombination-activating protein 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 625 amino acids
Theoretical weight: 71.72 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P15919 (Residues: 384-1008; Coverage: 60%)
Gene name: Rag1
Sequence domains: Recombination-activation protein 1 (RAG1), recombinase
V(D)J recombination-activating protein 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 359 amino acids
Theoretical weight: 40.04 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P21784 (Residues: 1-359; Coverage: 68%)
Gene names: Rag-2, Rag2
Sequence domains: Recombination activating protein 2
High mobility group protein B1 Chain: N
Molecule details ›
Chain: N
Length: 163 amino acids
Theoretical weight: 18.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09429 (Residues: 1-163; Coverage: 76%)
Gene names: HMG1, HMGB1
Sequence domains:
Nicked 12RSS intermediate reverse strand Chain: F
Molecule details ›
Chain: F
Length: 40 nucleotides
Theoretical weight: 12.43 KDa
DNA (5'-D(*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 10 nucleotides
Theoretical weight: 3.01 KDa
Nicked 12RSS intermediate forward strand Chain: L
Molecule details ›
Chain: L
Length: 30 nucleotides
Theoretical weight: 9.14 KDa
Intact 23RSS substrate reverse strand Chain: G
Molecule details ›
Chain: G
Length: 56 nucleotides
Theoretical weight: 17.26 KDa
Intact 23RSS substrate forward strand Chain: J
Molecule details ›
Chain: J
Length: 56 nucleotides
Theoretical weight: 17.25 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 156.678Å b: 123.562Å c: 186.286Å
α: 90° β: 105.6° γ: 90°
R-values:
R R work R free
0.216 0.214 0.254
Expression systems:
  • Homo sapiens
  • Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

RAG gene defects at the verge of immunodeficiency and immune dysregulation.
Villa et al. (2019)
14 more

1 mention without citation

Cutting antiparallel DNA strands in a single active site.
Chen et al. (2020)