› 5ze0

X-ray diffraction
2.75Å resolution

Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+

Released:
DOI: 10.2210/pdb5ze0/pdb
PDB entry 5ze0 coloured by chain, front view.
PDB entry 5ze0 coloured by chain, side view.
PDB entry 5ze0 coloured by chain, top view.
Source organism: Mus musculus
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

Assemblies composition:
hetero hexamer (preferred)
hetero pentamer
PDBe Complex ID:
PDB-CPX-219001 (preferred)
Entry contents:
3 distinct polypeptide molecules
6 distinct DNA molecules
Macromolecules (9 distinct):
V(D)J recombination-activating protein 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 627 amino acids
Theoretical weight: 71.87 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: 389 amino acids
Theoretical weight: 43.23 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P21784 (Residues: 1-387; Coverage: 73%)
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: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P63158 (Residues: 1-163; Coverage: 76%)
Gene names: Hmg-1, Hmg1, Hmgb1
Sequence domains:
DNA (45-MER) Chain: F
Molecule details ›
Chain: F
Length: 45 nucleotides
Theoretical weight: 13.98 KDa
DNA (5'-D(*AP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 16 nucleotides
Theoretical weight: 4.86 KDa
DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') Chain: J
Molecule details ›
Chain: J
Length: 16 nucleotides
Theoretical weight: 4.86 KDa
DNA (54-MER) Chain: G
Molecule details ›
Chain: G
Length: 54 nucleotides
Theoretical weight: 16.64 KDa
DNA (30-MER) Chain: L
Molecule details ›
Chain: L
Length: 30 nucleotides
Theoretical weight: 9.14 KDa
DNA (39-MER) Chain: M
Molecule details ›
Chain: M
Length: 39 nucleotides
Theoretical weight: 12.04 KDa

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand ZN 2 x ZN
Ligand EDO 3 x EDO
Ligand K 2 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 132.44Å b: 109.03Å c: 156.85Å
α: 90° β: 114.43° γ: 90°
R-values:
R R work R free
0.201 0.199 0.234
Expression systems:
  • Homo sapiens
  • Escherichia coli

Quick links

Citations

14 review citations

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

6 mentions without citation

Inner workings of RAG recombinase and its specialization for adaptive immunity.
Chen et al. (2021)
5 more