SMTL ID : 9q9i.1

Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

ADP.2: 23 residues within 4Å: Chain D: R.13, S.14, P.37, N.38, G.39, A.40, G.41, K.42, T.43, T.44, T.65, V.67, H.68, D.69 Chain E: D.1159, M.1188, K.1190, R.1200, C.1201, S.1202, Q.1205 Ligands: MG.1, BEF.4 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:R.13, D:S.14, D:G.39, D:G.39, D:A.40, D:G.41, D:K.42, D:T.43, D:T.44, D:T.65, D:D.69, E:K.1190, E:S.1202, E:Q.1205, E:Q.1205 Water bridges: D:T.43, D:Q.159, E:A.1203 Salt bridges: D:K.42 ADP.6: 25 residues within 4Å: Chain D: D.1159, M.1188, K.1190, R.1200, C.1201, S.1202, Q.1205 Chain E: R.13, S.14, P.37, N.38, G.39, A.40, G.41, K.42, T.43, T.44, E.47, T.65, V.67, H.68, D.69, K.1291 Ligands: BEF.3, MG.5 22 PLIP interactions: 16 interactions with chain E, 6 interactions with chain D Hydrogen bonds: E:R.13, E:S.14, E:S.14, E:G.39, E:G.39, E:A.40, E:G.41, E:K.42, E:T.43, E:T.44, E:E.47, E:T.65, E:D.69, E:K.1291, D:K.1190, D:S.1202, D:Q.1205, D:Q.1205 Salt bridges: E:K.42 pi-Stacking: E:H.68 Water bridges: D:A.1203, D:A.1203

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

BEF.3: 13 residues within 4Å: Chain D: S.1202, A.1203, G.1204, Q.1205, N.1236 Chain E: N.38, G.39, K.42, Q.159, E.1232, H.1269 Ligands: MG.5, ADP.6 No protein-ligand interaction detected (PLIP) BEF.4: 11 residues within 4Å: Chain D: N.38, G.39, K.42, Q.159, E.1232, H.1269 Chain E: S.1202, A.1203, G.1204 Ligands: MG.1, ADP.2 No protein-ligand interaction detected (PLIP)

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

MN.7: 5 residues within 4Å: Chain F: D.20, D.60, N.128, H.217, H.245 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.60, F:H.217 MN.8: 5 residues within 4Å: Chain G: D.60, N.128, N.129, H.217, H.245 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.60, G:H.217, G:H.245

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

Nibrin: C
DNA repair protein RAD50: DE
Double-strand break repair protein MRE11: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
F

D
A

E
B

F
D

G
E

Nibrin

DNA repair protein RAD50

Double-strand break repair protein MRE11

Related Entries With Identical Sequence