SMTL ID : 9bi4.1

cryo EM structure of dsDNA bound Mre11-Rad50 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 25 residues within 4Å: Chain A: R.13, S.14, M.35, N.36, G.37, S.38, G.39, K.40, T.41, T.42, V.63, I.65, D.67, I.70, Q.158, H.1272, R.1294 Chain B: D.1165, K.1193, R.1203, S.1205, A.1206, G.1207, Q.1208 Ligands: MG.2 23 PLIP interactions: 16 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.13, A:G.37, A:G.37, A:S.38, A:G.39, A:K.40, A:T.41, A:T.41, A:T.42, A:V.63, A:D.67, A:D.67, A:Q.158, A:R.1294, B:K.1193, B:R.1203, B:S.1205, B:A.1206, B:G.1207, B:Q.1208, B:Q.1208 Salt bridges: A:K.40, A:K.40 ATP.3: 25 residues within 4Å: Chain A: K.1193, R.1203, C.1204, S.1205, A.1206, G.1207, Q.1208, N.1239 Chain B: R.13, S.14, M.35, N.36, G.37, S.38, G.39, K.40, T.41, T.42, V.63, I.65, D.67, Q.158, H.1272, R.1294 Ligands: MG.4 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:R.13, B:G.37, B:S.38, B:G.39, B:G.39, B:K.40, B:T.41, B:T.42, B:I.65, B:D.67, B:Q.158, B:R.1294, B:R.1294, A:K.1193, A:S.1205, A:S.1205, A:A.1206, A:G.1207, A:Q.1208, A:Q.1208 Salt bridges: B:K.40, B:K.40

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.41, Q.158 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.41 MG.4: 3 residues within 4Å: Chain B: T.41, Q.158 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.41

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

MN.5: 5 residues within 4Å: Chain C: D.16, H.18, D.56, H.243 Ligands: MN.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.16, C:H.18, C:D.56, C:H.243 MN.6: 6 residues within 4Å: Chain C: D.16, D.56, N.124, H.213, H.241 Ligands: MN.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.56, C:H.213, C:H.241 MN.7: 5 residues within 4Å: Chain E: D.16, H.18, D.56, H.243 Ligands: MN.8 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.16, E:H.18, E:D.56, E:H.243 MN.8: 6 residues within 4Å: Chain E: D.16, D.56, N.124, H.213, H.241 Ligands: MN.7 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.56, E:H.213, E:H.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrini, J. et al., Structure guided functional analysis of the S. cerevisiae Mre11 complex. Res Sq (2024)

Release Date

2025-01-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
B

E
A

DNA repair protein RAD50

Double-strand break repair protein MRE11