SMTL ID : 9d4n.1

The cryo-EM structure of the yeast Dmc1 filament bound to ssDNA in the presence of ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 26 residues within 4Å: Chain A: E.122, F.123, R.124, C.125, G.126, K.127, T.128, Q.129, E.157, R.164, Q.167, R.305, I.324, G.325, E.326 Chain B: H.289, Q.310, D.311, S.312, P.313, D.314, M.315, P.316, E.317 Ligands: MG.2, MG.5 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.124, A:C.125, A:G.126, A:K.127, A:T.128, A:T.128, A:Q.129, A:Q.129, A:E.157, A:Q.167, A:R.305, B:A.288, B:D.314, B:M.315 Salt bridges: A:K.127, A:K.127, B:H.289 ATP.3: 25 residues within 4Å: Chain B: E.122, F.123, R.124, C.125, G.126, K.127, T.128, Q.129, E.157, R.164, Q.167, R.305, I.324 Chain C: A.288, H.289, Q.310, D.311, S.312, P.313, D.314, M.315, P.316, E.317 Ligands: MG.4, MG.8 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.124, B:C.125, B:G.126, B:K.127, B:T.128, B:T.128, B:Q.129, B:Q.129, B:R.305, C:A.288, C:H.289, C:P.313 Salt bridges: B:K.127, B:K.127, C:H.289 ATP.6: 24 residues within 4Å: Chain C: E.122, F.123, R.124, C.125, G.126, K.127, T.128, Q.129, R.164, Q.167, R.305, I.324 Chain D: A.288, H.289, Q.310, D.311, S.312, P.313, D.314, M.315, P.316, E.317 Ligands: MG.7, MG.11 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.124, C:R.124, C:C.125, C:G.126, C:K.127, C:T.128, C:Q.129, C:Q.167, C:R.305, D:A.288, D:M.315, D:E.317 Salt bridges: C:K.127, C:K.127, D:H.289 ATP.9: 25 residues within 4Å: Chain D: E.122, F.123, R.124, C.125, G.126, K.127, T.128, Q.129, E.157, R.164, Q.167, R.305, I.324 Chain E: A.288, H.289, Q.310, D.311, S.312, P.313, D.314, M.315, P.316, E.317 Ligands: MG.10, MG.14 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:R.124, D:C.125, D:G.126, D:K.127, D:T.128, D:Q.129, D:E.157, D:Q.167, D:R.305, E:A.288, E:M.315, E:E.317 Salt bridges: D:K.127, D:K.127, E:H.289 ATP.12: 25 residues within 4Å: Chain E: E.122, F.123, R.124, C.125, G.126, K.127, T.128, Q.129, E.157, R.164, Q.167, R.305, I.324 Chain F: A.288, H.289, Q.310, D.311, S.312, P.313, D.314, M.315, P.316, E.317 Ligands: MG.13, MG.17 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.124, E:C.125, E:G.126, E:K.127, E:T.128, E:T.128, E:Q.129, E:Q.129, E:Q.167, E:R.305, F:H.289 Salt bridges: E:K.127, E:K.127, F:H.289 ATP.15: 16 residues within 4Å: Chain F: E.122, F.123, R.124, C.125, G.126, K.127, T.128, Q.129, E.157, R.164, Q.167, R.305, I.324, G.325 Ligands: MG.16, MG.18 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:R.124, F:R.124, F:C.125, F:G.126, F:G.126, F:K.127, F:T.128, F:Q.129, F:Q.129, F:R.164, F:Q.167, F:Q.167, F:R.305 Salt bridges: F:K.127, F:K.127

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.128, E.157 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.128, A:E.157, A:E.157 MG.4: 3 residues within 4Å: Chain B: T.128, E.157 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.128, B:E.157 MG.5: 5 residues within 4Å: Chain B: A.288, H.289, S.291, D.311 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.288, B:S.291, B:D.311 MG.7: 2 residues within 4Å: Chain C: T.128 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.128 MG.8: 5 residues within 4Å: Chain C: A.288, H.289, S.291, D.311 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.288, C:S.291, C:D.311 MG.10: 3 residues within 4Å: Chain D: T.128, E.157 Ligands: ATP.9 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.128, D:E.157, D:E.157 MG.11: 5 residues within 4Å: Chain D: A.288, H.289, S.291, D.311 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:A.288, D:S.291, D:D.311 MG.13: 3 residues within 4Å: Chain E: T.128, E.157 Ligands: ATP.12 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.128, E:E.157, E:E.157 MG.14: 5 residues within 4Å: Chain E: A.288, H.289, S.291, D.311 Ligands: ATP.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:A.288, E:S.291, E:D.311 MG.16: 3 residues within 4Å: Chain F: T.128, E.157 Ligands: ATP.15 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.128, F:E.157, F:E.157 MG.17: 5 residues within 4Å: Chain F: A.288, H.289, S.291, D.311 Ligands: ATP.12 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:A.288, F:H.289, F:S.291, F:D.311 MG.18: 1 residues within 4Å: Ligands: ATP.15 No protein-ligand interaction detected (PLIP)

Links

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Citation

Shin, Y. et al., The cryo-EM structure of the yeast RAD51 filament bound to ssDNA in the presence of ATP. To Be Published

Release Date

2025-01-22

Peptides

Meiotic recombination protein DMC1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Meiotic recombination protein DMC1

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