SMTL ID : 9q9h.1

Cryo-EM structure of human Mre11-Rad50 complex bound to DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.43, Q.159, D.1231 Ligands: ADP.2, BEF.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.43, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain B: T.43, Q.159 Ligands: ADP.4, BEF.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.43, H2O.1, H2O.1

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 21 residues within 4Å: Chain A: R.13, S.14, P.37, G.39, A.40, G.41, K.42, T.43, T.44, T.65, V.67, H.68, D.69, Q.159 Chain B: D.1159, K.1190, R.1200, S.1202, Q.1205 Ligands: MG.1, BEF.5 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.13, A:S.14, A:P.37, A:G.39, A:A.40, A:K.42, A:T.43, A:T.44, A:T.44, A:T.65, A:H.68, A:D.69, A:K.1291, B:R.1200, B:S.1202, B:Q.1205, B:Q.1205 Salt bridges: A:K.42 Water bridges: B:A.1203, B:A.1203 ADP.4: 23 residues within 4Å: Chain A: D.1159, M.1188, K.1190, R.1200, S.1202, Q.1205 Chain B: R.13, S.14, P.37, N.38, G.39, G.41, K.42, T.43, T.44, T.65, V.67, H.68, D.69, Q.159, K.1291 Ligands: MG.3, BEF.6 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.13, B:S.14, B:G.39, B:G.41, B:K.42, B:T.43, B:T.44, B:T.44, B:T.65, B:D.69, B:K.1291, A:D.1159, A:K.1190, A:Q.1205, A:Q.1205 Salt bridges: B:K.42 Water bridges: A:A.1203, A:A.1203

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)(Non-covalent)

BEF.5: 13 residues within 4Å: Chain A: N.38, K.42, T.43, Q.159, E.1232, H.1269 Chain B: S.1202, A.1203, G.1204, Q.1205, N.1236 Ligands: MG.1, ADP.2 No protein-ligand interaction detected (PLIP) BEF.6: 12 residues within 4Å: Chain A: S.1202, A.1203, G.1204, N.1236 Chain B: N.38, K.42, T.43, Q.159, E.1232, H.1269 Ligands: MG.3, ADP.4 No protein-ligand interaction detected (PLIP)

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.7: 5 residues within 4Å: Chain C: D.20, H.22, D.60, H.247 Ligands: MN.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.20, C:H.22, C:D.60, C:H.247 MN.8: 5 residues within 4Å: Chain C: D.60, N.128, H.217, H.245 Ligands: MN.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.60, C:H.217, C:H.245 MN.9: 6 residues within 4Å: Chain D: D.20, D.60, N.128, H.217, H.245 Ligands: MN.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.60, D:H.217, D:H.245 MN.10: 6 residues within 4Å: Chain D: D.20, H.22, D.60, H.245, H.247 Ligands: MN.9 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.20, D:H.22, D:D.60, D:H.247, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, Y. et al., Structural basis for DNA break sensing by human MRE11-RAD50-NBS1 and its regulation by telomeric factor TRF2. Nat Commun (2025)

Release Date

2025-10-01

Peptides

DNA repair protein RAD50: AB
Double-strand break repair protein MRE11: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

DNA repair protein RAD50

Double-strand break repair protein MRE11

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