SMTL ID : 6lod.1

Cryo-EM structure of the air-oxidized photosynthetic alternative complex III from Roseiflexus castenholzii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 23 residues within 4Å: Chain A: G.59, G.60, F.61, L.65, H.66, L.69, M.71, Y.75, P.89, T.93, C.94, C.97, H.98, I.101, I.102, K.107, V.108, F.110, W.123 Chain E: V.84, V.96, L.99 Ligands: HEC.4 26 PLIP interactions: 22 interactions with chain A, 4 interactions with chain E, Hydrophobic interactions: A:F.61, A:F.61, A:L.65, A:L.69, A:Y.75, A:P.89, A:I.101, A:I.102, A:I.102, A:V.108, A:F.110, A:W.123, E:V.84, E:V.96, E:V.96, E:L.99 Salt bridges: A:K.107 pi-Stacking: A:F.61, A:H.66, A:H.66, A:H.98, A:H.98, A:H.98 pi-Cation interactions: A:H.98, A:H.98 Metal complexes: A:H.66 HEC.2: 28 residues within 4Å: Chain A: R.48, P.130, F.132, V.133, L.166, F.167, M.168, C.171, L.172, H.175, T.219, N.220, C.221, C.224, H.225 Chain B: A.762, V.765, V.775, N.777, R.778 Chain C: W.150, L.158, M.160 Chain D: Y.97, L.99 Chain E: H.3, Y.7 Ligands: HEC.5 16 PLIP interactions: 2 interactions with chain D, 8 interactions with chain A, 2 interactions with chain E, 3 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: D:Y.97, D:L.99, A:F.132, A:F.132, A:V.133, A:V.133, A:M.168, A:L.172, B:V.765, B:V.775, B:R.778, C:L.158 Salt bridges: A:R.48, E:H.3 Metal complexes: A:H.225 Hydrogen bonds: E:Y.7 HEC.3: 25 residues within 4Å: Chain A: C.73, H.77, V.80, H.85, A.86, N.87, I.88, K.125, H.127, L.129, F.135, H.137, H.140, V.141, V.145, G.146, C.147, C.150, H.151, L.166, F.189 Chain B: I.12 Chain E: Q.15 Ligands: HEC.4, HEC.5 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:H.77, A:V.80, A:V.80, A:A.86, A:I.88, A:H.127, A:L.129, A:F.135, A:F.135, A:V.141, A:V.145, A:L.166, A:F.189 Hydrogen bonds: A:A.86, A:I.88, A:L.129 Salt bridges: A:H.85, A:K.125, A:K.125, A:K.131 pi-Stacking: A:F.135 pi-Cation interactions: A:H.127 Metal complexes: A:H.151 HEC.4: 22 residues within 4Å: Chain A: Q.56, F.61, H.63, V.67, M.71, C.73, C.76, H.77, I.88, P.89, W.123, N.124, K.125, V.126, H.127, C.147, H.151, I.154, V.160, M.191 Ligands: HEC.1, HEC.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.61, A:F.61, A:F.61, A:F.61, A:F.61, A:V.67, A:M.71, A:I.88, A:W.123, A:W.123, A:W.123, A:V.126, A:I.154, A:I.154, A:V.160 Hydrogen bonds: A:V.126, A:H.127 Metal complexes: A:H.63, A:H.77 HEC.5: 24 residues within 4Å: Chain A: V.133, F.135, N.136, I.139, H.140, K.143, V.145, C.150, W.170, C.171, C.174, H.175, Y.181, V.182, I.212, R.213, L.218, I.223, C.224 Chain B: R.852, I.853, R.856 Ligands: HEC.2, HEC.3 26 PLIP interactions: 23 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:V.133, A:N.136, A:I.139, A:K.143, A:V.145, A:W.170, A:W.170, A:Y.181, A:V.182, A:I.212, A:I.212, A:L.218, A:I.223, B:I.853 Hydrogen bonds: A:R.213 Salt bridges: A:K.143, A:R.213, A:R.213, B:R.852, B:R.856 pi-Stacking: A:F.135, A:H.140, A:H.175, A:H.175 Metal complexes: A:H.140, A:H.175 HEC.12: 20 residues within 4Å: Chain A: Y.75 Chain E: Y.81, C.82, C.85, H.86, L.100, P.102, P.104, P.105, F.107, R.111, L.112, V.123, L.124, R.128, R.129, T.130, M.131, Y.134, I.151 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:F.107, E:L.112, E:L.112, E:V.123, E:L.124, E:R.128, E:T.130, E:I.151 Hydrogen bonds: E:T.130 Salt bridges: E:R.111, E:R.128, E:R.129, E:R.129 Metal complexes: E:H.86

2 x EL6: [(2S)-2-octadecanoyloxypropyl] octadecanoate(Covalent)

EL6.6: 7 residues within 4Å: Chain B: C.1 Chain C: L.62, A.66, F.69, L.139, P.145, W.146 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.62, C:F.69, C:F.69, C:F.69, C:L.139, C:W.146 EL6.11: 7 residues within 4Å: Chain A: L.34, V.37, F.41 Chain B: L.5 Chain C: Y.149, S.176 Chain E: C.2 8 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:L.5, A:L.34, A:V.37, A:V.37, A:F.41, A:F.41, A:F.41, C:Y.149

3 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.7: 12 residues within 4Å: Chain B: C.692, N.693, S.694, C.695, N.696, A.697, C.698, I.727, C.875, T.877, A.879, I.880 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.692, B:C.695, B:C.698, B:C.875 SF4.8: 11 residues within 4Å: Chain B: M.685, C.702, N.706, W.724, I.725, L.746, C.841, F.843, C.844, T.869, C.871 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.702, B:C.841, B:C.844, B:C.871 SF4.9: 14 residues within 4Å: Chain B: C.747, Q.748, Q.749, C.750, A.753, P.754, C.755, N.772, C.789, P.790, Y.791, V.793, R.794, K.840 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.747, B:C.750, B:C.755, B:C.789

1 x F3S: FE3-S4 CLUSTER(Covalent)

F3S.10: 12 residues within 4Å: Chain B: V.758, C.759, P.760, V.761, A.763, T.764, C.779, V.780, G.781, T.782, C.785, M.838 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.759, B:C.779, B:T.782, B:C.785

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from Roseiflexus castenholzii . Sci Adv (2020)

Release Date

2020-11-04

Peptides

MULTIHEME_CYTC domain-containing protein: A
Fe-S-cluster-containing hydrogenase components 1-like protein: B
Polysulphide reductase NrfD: C
Uncharacterized protein ActD: D
Cytochrome c domain-containing protein: E
Uncharacterized protein ActF: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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MULTIHEME_CYTC domain-containing protein

Fe-S-cluster-containing hydrogenase components 1-like protein

Polysulphide reductase NrfD

Uncharacterized protein ActD

Cytochrome c domain-containing protein

Uncharacterized protein ActF

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