SMTL ID : 9q9j.1

Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

ADP.2: 21 residues within 4Å: Chain E: 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 F: M.1188, K.1190, R.1200, S.1202, Q.1205 Ligands: MG.1, BEF.4 22 PLIP interactions: 16 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:R.13, 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:T.44, E:T.65, E:D.69, E:D.69, F:K.1190, F:S.1202, F:Q.1205, F:Q.1205 Water bridges: E:T.43, E:Q.159, F:A.1203, F:A.1203 Salt bridges: E:K.42 ADP.6: 20 residues within 4Å: Chain E: K.1190, R.1200, S.1202, Q.1205 Chain F: 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 Ligands: BEF.3, MG.5 22 PLIP interactions: 15 interactions with chain F, 7 interactions with chain E Hydrogen bonds: F:R.13, F:S.14, F:G.39, F:G.39, F:A.40, F:G.41, F:K.42, F:T.43, F:T.44, F:T.44, F:T.65, F:D.69, E:K.1190, E:R.1200, E:S.1202, E:Q.1205, E:Q.1205 Water bridges: F:T.43, F:Q.159, E:A.1203, E:A.1203 Salt bridges: F:K.42

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

BEF.3: 13 residues within 4Å: Chain E: S.1202, A.1203, G.1204, N.1236 Chain F: N.38, G.39, K.42, T.43, Q.159, E.1232, H.1269 Ligands: MG.5, ADP.6 No protein-ligand interaction detected (PLIP) BEF.4: 14 residues within 4Å: Chain E: N.38, G.39, K.42, T.43, Q.159, E.1232, H.1269 Chain F: S.1202, A.1203, G.1204, Q.1205, N.1236 Ligands: MG.1, ADP.2 No protein-ligand interaction detected (PLIP)

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

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

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

Telomeric repeat-binding factor 2: A
Nibrin: D
DNA repair protein RAD50: EF
Double-strand break repair protein MRE11: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

D
F

E
A

F
B

G
D

H
E

Telomeric repeat-binding factor 2

Nibrin

DNA repair protein RAD50

Double-strand break repair protein MRE11

Related Entries With Identical Sequence