SMTL ID : 6dbj.1

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.877, C.880, H.1087, H.1092 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.877, A:C.880, A:H.1087, A:H.1092 ZN.4: 4 residues within 4Å: Chain C: C.877, C.880, H.1087, H.1092 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.877, C:C.880, C:H.1087, C:H.1092

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.748, G.749, E.1112, N.1115 Chain G: G.15, T.16 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.748, A:G.749 CA.3: 5 residues within 4Å: Chain A: D.748, E.812, D.858 Chain G: T.16 Chain I: A.16 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.748, A:D.858 CA.5: 6 residues within 4Å: Chain C: D.748, G.749, E.1112, N.1115 Chain F: G.15, T.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.748, C:G.749 CA.6: 5 residues within 4Å: Chain C: D.748, E.812, D.858 Chain F: T.16 Chain J: A.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.748, C:D.858

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ru, H. et al., DNA melting initiates the RAG catalytic pathway. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-08-01

Peptides

Recombination activating gene 1 - MBP chimera: AC
Recombination activating gene 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Recombination activating gene 1 - MBP chimera

Recombination activating gene 2

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