SMTL ID : 6dbv.1

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.29 Å

Oligo State

hetero-1-2-1-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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.877, A:H.1087, A:H.1092 ZN.4: 5 residues within 4Å: Chain C: C.880, H.894, S.895, I.896, H.1092 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.894, C:S.895

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.748, H.945, E.1112 Chain E: C.17 Ligands: CA.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.748, A:E.1112 CA.3: 3 residues within 4Å: Chain A: E.1112 Chain E: C.17 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.1112, A:E.1112 CA.5: 4 residues within 4Å: Chain C: D.748, G.749, E.1112 Ligands: CA.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.748 CA.6: 4 residues within 4Å: Chain C: D.748, D.858 Chain H: A.47 Ligands: CA.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.748, C:D.748

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: A
Recombination activating gene 2: BD
Recombination activating gene 1 - MBP chimera: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

Recombination activating gene 1 - MBP chimera

Recombination activating gene 2

Recombination activating gene 1 - MBP chimera

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