SMTL ID : 6rd5.1

CryoEM structure of Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-mer

Ligands

22 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.1: 19 residues within 4Å: Chain A: Q.13, P.15, A.16, G.17, L.18, S.19, A.20, A.27, C.31 Chain D: S.20, W.24 Chain E: Q.74 Chain F: F.32, L.40 Chain H: R.98 Chain M: F.80 Ligands: PEV.2, PEV.3, PEV.13 Ligand excluded by PLIP PEV.2: 21 residues within 4Å: Chain A: A.20, G.24, A.27, L.28, C.31, T.32, G.33, R.34 Chain D: S.7, Q.9, A.13, A.16, V.17 Chain F: L.48, G.49, F.51, T.52, I.55 Ligands: PEV.1, LMT.10, PEV.13 Ligand excluded by PLIP PEV.3: 22 residues within 4Å: Chain A: G.11, F.12, F.14, L.18 Chain E: G.70, S.72, A.75, I.77, A.78, L.79, G.81, A.82, L.113, F.116, S.117, I.120, F.122 Ligands: PEV.1, PEV.4, PEV.8, PEV.15, PEV.18 Ligand excluded by PLIP PEV.4: 14 residues within 4Å: Chain A: F.12 Chain B: S.322, S.323, F.324, L.325, K.327 Chain H: P.106, F.109, L.110 Ligands: PEV.3, LMT.6, PEV.8, PEV.15, PEV.18 Ligand excluded by PLIP PEV.7: 8 residues within 4Å: Chain E: W.112, L.119, P.121 Chain G: G.34, H.41 Chain H: C.279, S.282, A.283 Ligand excluded by PLIP PEV.8: 13 residues within 4Å: Chain A: I.25, N.29 Chain E: G.81, W.85, I.86, Y.88 Chain H: P.169, N.171, E.172, P.174 Ligands: PEV.3, PEV.4, PEV.18 Ligand excluded by PLIP PEV.9: 14 residues within 4Å: Chain B: A.320, S.323, L.326 Chain E: F.122, A.124, V.125, A.128, F.129 Chain H: K.101, S.104, L.105, V.293 Ligands: LMT.6, LMT.20 Ligand excluded by PLIP PEV.11: 12 residues within 4Å: Chain D: L.4, L.8 Chain F: Y.58, L.61, L.64, R.65, K.71 Chain H: L.178, T.182, V.234, W.241 Ligands: LMT.12 Ligand excluded by PLIP PEV.13: 10 residues within 4Å: Chain F: T.30, S.31, F.32, Y.33, A.36, T.37, I.41 Ligands: PEV.1, PEV.2, LMT.10 Ligand excluded by PLIP PEV.15: 18 residues within 4Å: Chain B: F.324 Chain E: G.70, A.110, L.113, I.114, S.117 Chain G: T.4, L.7, G.8, F.11, Y.14, F.15, F.18 Chain K: V.89 Ligands: PEV.3, PEV.4, LMT.14, LMT.16 Ligand excluded by PLIP PEV.18: 25 residues within 4Å: Chain A: F.12, Q.13, F.14, P.15, L.18, V.22, I.25 Chain D: T.14, V.18, W.21, H.25, Q.29, L.30, T.33 Chain H: R.98, V.100, S.104, P.106, T.107, C.162, L.165, P.174 Ligands: PEV.3, PEV.4, PEV.8 Ligand excluded by PLIP PEV.21: 19 residues within 4Å: Chain E: F.80 Chain I: Q.13, P.15, A.16, G.17, L.18, S.19, A.20, A.27, C.31 Chain L: S.20, W.24 Chain M: Q.74 Chain N: F.32, L.40 Chain P: R.98 Ligands: PEV.22, PEV.23, PEV.33 Ligand excluded by PLIP PEV.22: 21 residues within 4Å: Chain I: A.20, G.24, A.27, L.28, C.31, T.32, G.33, R.34 Chain L: S.7, Q.9, A.13, A.16, V.17 Chain N: L.48, G.49, F.51, T.52, I.55 Ligands: PEV.21, LMT.30, PEV.33 Ligand excluded by PLIP PEV.23: 22 residues within 4Å: Chain I: G.11, F.12, F.14, L.18 Chain M: G.70, S.72, A.75, I.77, A.78, L.79, G.81, A.82, L.113, F.116, S.117, I.120, F.122 Ligands: PEV.21, PEV.24, PEV.28, PEV.35, PEV.38 Ligand excluded by PLIP PEV.24: 14 residues within 4Å: Chain I: F.12 Chain J: S.322, S.323, F.324, L.325, K.327 Chain P: P.106, F.109, L.110 Ligands: PEV.23, LMT.26, PEV.28, PEV.35, PEV.38 Ligand excluded by PLIP PEV.27: 8 residues within 4Å: Chain M: W.112, L.119, P.121 Chain O: G.34, H.41 Chain P: C.279, S.282, A.283 Ligand excluded by PLIP PEV.28: 13 residues within 4Å: Chain I: I.25, N.29 Chain M: G.81, W.85, I.86, Y.88 Chain P: P.169, N.171, E.172, P.174 Ligands: PEV.23, PEV.24, PEV.38 Ligand excluded by PLIP PEV.29: 14 residues within 4Å: Chain J: A.320, S.323, L.326 Chain M: F.122, A.124, V.125, A.128, F.129 Chain P: K.101, S.104, L.105, V.293 Ligands: LMT.26, LMT.40 Ligand excluded by PLIP PEV.31: 12 residues within 4Å: Chain L: L.4, L.8 Chain N: Y.58, L.61, L.64, R.65, K.71 Chain P: L.178, T.182, V.234, W.241 Ligands: LMT.32 Ligand excluded by PLIP PEV.33: 10 residues within 4Å: Chain N: T.30, S.31, F.32, Y.33, A.36, T.37, I.41 Ligands: PEV.21, PEV.22, LMT.30 Ligand excluded by PLIP PEV.35: 18 residues within 4Å: Chain C: V.89 Chain J: F.324 Chain M: G.70, A.110, L.113, I.114, S.117 Chain O: T.4, L.7, G.8, F.11, Y.14, F.15, F.18 Ligands: PEV.23, PEV.24, LMT.34, LMT.36 Ligand excluded by PLIP PEV.38: 25 residues within 4Å: Chain I: F.12, Q.13, F.14, P.15, L.18, V.22, I.25 Chain L: T.14, V.18, W.21, H.25, Q.29, L.30, T.33 Chain P: R.98, V.100, S.104, P.106, T.107, C.162, L.165, P.174 Ligands: PEV.23, PEV.24, PEV.28 Ligand excluded by PLIP

16 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.5: 14 residues within 4Å: Chain E: G.131, M.132, P.134, A.137 Chain H: G.112, V.113, R.115, F.116, F.156, L.294, G.297, V.298 Ligands: LMT.6, LMT.20 Ligand excluded by PLIP LMT.6: 11 residues within 4Å: Chain E: F.127, A.128, G.131, M.132 Chain H: F.109, I.160, L.164 Ligands: PEV.4, LMT.5, PEV.9, LMT.20 Ligand excluded by PLIP LMT.10: 11 residues within 4Å: Chain F: I.41, P.42, W.45, Y.46, G.49, F.53, T.56 Chain H: I.194, F.202 Ligands: PEV.2, PEV.13 Ligand excluded by PLIP LMT.12: 5 residues within 4Å: Chain F: G.59, I.60, L.61, L.64 Ligands: PEV.11 Ligand excluded by PLIP LMT.14: 11 residues within 4Å: Chain A: A.64, F.65, K.67 Chain E: L.103, N.106, V.107, A.110 Chain G: A.55, N.56 Chain H: F.170 Ligands: PEV.15 Ligand excluded by PLIP LMT.16: 8 residues within 4Å: Chain E: I.114, S.117, S.118 Chain G: Y.14, F.15, V.37, R.40 Ligands: PEV.15 Ligand excluded by PLIP LMT.19: 7 residues within 4Å: Chain H: F.116, Q.120, N.121, I.301, T.304, V.305 Ligands: LMT.20 Ligand excluded by PLIP LMT.20: 8 residues within 4Å: Chain H: R.115, F.116, S.119, L.290 Ligands: LMT.5, LMT.6, PEV.9, LMT.19 Ligand excluded by PLIP LMT.25: 14 residues within 4Å: Chain M: G.131, M.132, P.134, A.137 Chain P: G.112, V.113, R.115, F.116, F.156, L.294, G.297, V.298 Ligands: LMT.26, LMT.40 Ligand excluded by PLIP LMT.26: 11 residues within 4Å: Chain M: F.127, A.128, G.131, M.132 Chain P: F.109, I.160, L.164 Ligands: PEV.24, LMT.25, PEV.29, LMT.40 Ligand excluded by PLIP LMT.30: 11 residues within 4Å: Chain N: I.41, P.42, W.45, Y.46, G.49, F.53, T.56 Chain P: I.194, F.202 Ligands: PEV.22, PEV.33 Ligand excluded by PLIP LMT.32: 5 residues within 4Å: Chain N: G.59, I.60, L.61, L.64 Ligands: PEV.31 Ligand excluded by PLIP LMT.34: 11 residues within 4Å: Chain I: A.64, F.65, K.67 Chain M: L.103, N.106, V.107, A.110 Chain O: A.55, N.56 Chain P: F.170 Ligands: PEV.35 Ligand excluded by PLIP LMT.36: 8 residues within 4Å: Chain M: I.114, S.117, S.118 Chain O: Y.14, F.15, V.37, R.40 Ligands: PEV.35 Ligand excluded by PLIP LMT.39: 7 residues within 4Å: Chain P: F.116, Q.120, N.121, I.301, T.304, V.305 Ligands: LMT.40 Ligand excluded by PLIP LMT.40: 8 residues within 4Å: Chain P: R.115, F.116, S.119, L.290 Ligands: LMT.25, LMT.26, PEV.29, LMT.39 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.17: 2 residues within 4Å: Chain H: H.248, H.252 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.248, H:H.252, H2O.2 ZN.37: 2 residues within 4Å: Chain P: H.248, H.252 3 PLIP interactions: 2 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:H.248, P:H.252, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murphy, B.J. et al., Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling. Science (2019)

Release Date

2019-07-03

Peptides

ASA-10: Polytomella F-ATP synthase associated subunit 10: AI
ATP synthase associated protein ASA1: BJ
Mitochondrial F1F0 ATP synthase associated 32 kDa protein: CK
Mitochondrial F1F0 ATP synthase associated 14 kDa protein: DL
Mitochondrial ATP synthase subunit ASA6: EM
Mitochondrial ATP synthase subunit ASA8: FN
Mitochondrial ATP synthase subunit ASA9: GO
Mitochondrial ATP synthase subunit 6: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

I
0

B
1

J
1

C
3

K
3

D
5

L
5

E
6

M
6

F
8

N
8

G
9

O
9

H
M

P
M

ASA-10: Polytomella F-ATP synthase associated subunit 10

ATP synthase associated protein ASA1

Mitochondrial F1F0 ATP synthase associated 32 kDa protein

Mitochondrial F1F0 ATP synthase associated 14 kDa protein

Mitochondrial ATP synthase subunit ASA6

Mitochondrial ATP synthase subunit ASA8

Mitochondrial ATP synthase subunit ASA9

Mitochondrial ATP synthase subunit 6

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