6cij

Electron Microscopy
3.9Å resolution

Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)

Released:
Source organisms:
Related structures: EMD-7480

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:

Structure analysis Details

Assembly composition:
hetero 11-mer (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: 776 amino acids
Theoretical weight: 88.67 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P15919 (Residues: 265-1040; Coverage: 75%)
Gene name: Rag1
Sequence domains:
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 K-12
UniProt:
  • Canonical: P09429 (Residues: 1-163; Coverage: 76%)
Gene names: HMG1, HMGB1
Sequence domains:
V(D)J recombination-activating protein 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 520 amino acids
Theoretical weight: 58.16 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: P21784 (Residues: 1-520; Coverage: 99%)
Gene names: Rag-2, Rag2
Sequence domains:
DNA (46-MER) Chain: F
Molecule details ›
Chain: F
Length: 46 nucleotides
Theoretical weight: 14.27 KDa
DNA (5'-D(*GP*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: 4.88 KDa
DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') Chain: J
Molecule details ›
Chain: J
Length: 20 nucleotides
Theoretical weight: 6.09 KDa
DNA (60-MER) Chain: G
Molecule details ›
Chain: G
Length: 61 nucleotides
Theoretical weight: 18.81 KDa
DNA (30-MER) Chain: L
Molecule details ›
Chain: L
Length: 30 nucleotides
Theoretical weight: 9.14 KDa
DNA (41-MER) Chain: M
Molecule details ›
Chain: M
Length: 41 nucleotides
Theoretical weight: 12.66 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-7480
Expression systems:
  • Homo sapiens
  • Escherichia coli K-12