› 3gna

X-ray diffraction
2.4Å resolution

Crystal structure of the RAG1 nonamer-binding domain with DNA

Released:
DOI: 10.2210/pdb3gna/pdb
PDB entry 3gna coloured by chain, front view.
PDB entry 3gna coloured by chain, side view.
PDB entry 3gna coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis.
Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG
Nat Struct Mol Biol 16 499-508 (2009)
PMID: 19396172

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116311 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
V(D)J recombination-activating protein 1 Chain: A
Molecule details ›
Chain: A
Length: 96 amino acids
Theoretical weight: 10.81 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P15919 (Residues: 389-464; Coverage: 7%)
Gene name: Rag1
Structure domains: Helix Hairpins
5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 14 nucleotides
Theoretical weight: 4.23 KDa
Source organism: Mus musculus
Expression system: Not provided
5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3' Chain: E
Molecule details ›
Chain: E
Length: 14 nucleotides
Theoretical weight: 4.33 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: I422
Unit cell:
a: 97.47Å b: 97.47Å c: 69.78Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.236 0.271
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Recombination centres and the orchestration of V(D)J recombination.
Schatz et al. (2011)
12 more

9 mentions without citation

Riches in RAGs: Revealing the V(D)J Recombinase through High-Resolution Structures.
Rodgers KK. (2017)
8 more