SMTL ID : 7r0w.1

2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 25 residues within 4Å: Chain B: Q.54, F.55, G.58, F.59, M.61, T.62, Y.65, V.76, R.90, H.93, R.94, A.97, M.100, T.135, F.138, G.139, G.142, L.145, P.146, Y.191, H.194, T.195, P.199 Chain C: E.78 Chain I: F.196 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.55, B:T.62, B:Y.65, B:Y.65, B:R.94, B:A.97, B:T.135, B:F.138, B:F.138, B:F.138, B:L.145, B:Y.191, B:T.195, B:P.199 Salt bridges: B:R.90, B:R.90, B:R.94 Metal complexes: B:H.93, B:H.194 HEM.2: 21 residues within 4Å: Chain B: V.37, N.38, Y.41, C.42, G.45, L.48, T.49, F.210, I.213, R.214, G.217, I.218 Chain C: N.25, D.35, M.39, F.40, C.43, I.44 Chain H: R.26 Ligands: HEM.3, PL9.6 17 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: B:V.37, B:V.37, B:Y.41, B:L.48, B:F.210, B:F.210, B:R.214, B:I.218, C:M.39, C:F.40, C:I.44, C:I.44 Hydrogen bonds: B:I.218 Salt bridges: B:R.214 pi-Stacking: C:F.40, C:F.40 Metal complexes: H2O.1 HEM.3: 27 residues within 4Å: Chain B: Y.41, G.44, G.45, T.47, L.48, M.100, M.104, H.107, V.108, R.110, V.111, G.116, R.121, T.124, W.125, G.128, V.129, A.132, T.135, L.206, H.209, F.210, I.213, G.217, I.218, S.219 Ligands: HEM.2 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:T.47, B:V.108, B:V.108, B:V.111, B:V.111, B:T.124, B:W.125, B:W.125, B:W.125, B:V.129, B:A.132, B:L.206, B:F.210, B:I.218 Hydrogen bonds: B:G.44, B:G.45, B:S.219 Salt bridges: B:H.107, B:R.110, B:R.110, B:R.121 Metal complexes: B:H.209 HEM.12: 27 residues within 4Å: Chain I: Y.41, G.44, G.45, T.47, L.48, M.100, M.104, H.107, V.108, R.110, V.111, G.116, R.121, T.124, W.125, G.128, V.129, L.131, A.132, L.206, H.209, F.210, I.213, G.217, I.218, S.219 Ligands: HEM.16 23 PLIP interactions: 23 interactions with chain I, Hydrophobic interactions: I:T.47, I:L.48, I:V.108, I:V.111, I:V.111, I:T.124, I:W.125, I:W.125, I:V.129, I:L.131, I:A.132, I:L.206, I:F.210, I:I.213, I:I.218 Hydrogen bonds: I:G.44, I:G.45, I:S.219 Salt bridges: I:H.107, I:R.110, I:R.110, I:R.121 Metal complexes: I:H.209 HEM.13: 24 residues within 4Å: Chain B: F.196 Chain I: F.51, Q.54, F.55, G.58, M.61, T.62, Y.65, V.76, R.90, H.93, R.94, A.97, T.135, F.138, G.139, G.142, L.145, P.146, Y.191, H.194, T.195, P.199 Chain J: E.78 19 PLIP interactions: 19 interactions with chain I, Hydrophobic interactions: I:F.51, I:F.55, I:T.62, I:Y.65, I:Y.65, I:A.97, I:T.135, I:F.138, I:F.138, I:F.138, I:L.145, I:Y.191, I:T.195, I:P.199 Salt bridges: I:R.90, I:R.90, I:R.94 Metal complexes: I:H.93, I:H.194 HEM.16: 20 residues within 4Å: Chain I: V.37, N.38, Y.41, C.42, G.45, L.48, T.49, F.210, I.213, R.214, G.217, I.218 Chain J: N.25, M.39, F.40, C.43, I.44 Chain P: R.26 Ligands: HEM.12, PL9.14 16 PLIP interactions: 9 interactions with chain I, 6 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:V.37, I:V.37, I:L.48, I:F.210, I:F.210, I:I.213, J:M.39, J:F.40, J:I.44, J:I.44 Hydrogen bonds: I:I.218, J:N.25 Salt bridges: I:K.31, I:R.214 pi-Stacking: J:F.40 Metal complexes: H2O.1

4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.4: 18 residues within 4Å: Chain B: V.83, N.84, F.85, W.87, L.88, I.92 Chain C: A.52, I.56 Chain D: N.290, R.293, F.296, L.299, F.300 Chain Q: G.41, V.42, G.45, A.46, Y.48 16 PLIP interactions: 4 interactions with chain Q, 4 interactions with chain B, 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: Q:V.42, Q:A.46, Q:Y.48, Q:Y.48, B:F.85, B:L.88, D:F.296, D:F.296, D:F.296, D:L.299, D:F.300, C:A.52 Hydrogen bonds: B:V.83, B:F.85, D:N.290 Salt bridges: D:R.293 PGV.8: 14 residues within 4Å: Chain C: A.103, I.104, G.107, V.111, I.114, E.115, N.118, R.125, R.126, P.127, I.128, A.129, V.132 Ligands: CLA.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.111, C:E.115 Hydrogen bonds: C:R.125, C:I.128, C:A.129 PGV.19: 14 residues within 4Å: Chain I: K.118 Chain J: I.87, A.103, I.104, G.107, L.108, I.114, E.115, N.118, R.126, I.128, A.129, V.132 Ligands: CLA.17 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.87, J:I.104, J:L.108 Hydrogen bonds: J:N.118, J:I.128, J:A.129 Salt bridges: I:K.118 PGV.20: 24 residues within 4Å: Chain I: A.56, T.57, V.83, N.84, F.85, W.87, L.88, I.92 Chain J: A.52, I.56 Chain K: N.290, T.292, R.293, F.296, L.297, L.299, F.300 Chain L: G.41, V.42, G.45, A.46, Y.48, P.49 Ligands: PL9.14 17 PLIP interactions: 5 interactions with chain I, 1 interactions with chain J, 4 interactions with chain L, 7 interactions with chain K Hydrophobic interactions: I:A.56, I:T.57, I:L.88, I:I.92, J:I.56, L:A.46, L:Y.48, L:Y.48, L:P.49, K:F.296, K:F.296, K:F.296, K:F.300, K:F.300 Hydrogen bonds: I:F.85, K:N.290 Salt bridges: K:R.293

2 x ECH: beta,beta-caroten-4-one(Non-covalent)

ECH.5: 24 residues within 4Å: Chain B: I.39, F.40, L.46, M.103, L.106 Chain C: C.43, L.50 Chain F: T.18, L.19, L.22 Chain G: L.13, V.16, T.17, A.19, G.20, V.23, Y.26, L.27 Chain H: F.15, S.18, I.19, V.22, F.29 Ligands: 6PL.11 20 PLIP interactions: 3 interactions with chain F, 4 interactions with chain H, 5 interactions with chain G, 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: F:T.18, F:L.19, F:L.22, H:F.15, H:I.19, H:V.22, H:F.29, G:L.13, G:L.13, G:V.23, G:Y.26, G:L.27, B:I.39, B:I.39, B:I.39, B:F.40, B:F.40, B:L.46, B:L.106, C:L.50 ECH.15: 22 residues within 4Å: Chain I: I.39, F.40, C.42, L.43, L.46, M.103, L.106 Chain J: C.43, L.50 Chain N: T.18, L.19, L.22 Chain O: L.13, V.16, T.17, A.19, G.20, V.23 Chain P: F.15, S.18, I.19, V.22 19 PLIP interactions: 8 interactions with chain I, 4 interactions with chain N, 3 interactions with chain P, 1 interactions with chain J, 3 interactions with chain O Hydrophobic interactions: I:I.39, I:I.39, I:I.39, I:F.40, I:F.40, I:L.43, I:L.46, I:L.106, N:T.18, N:L.19, N:L.22, N:L.22, P:F.15, P:I.19, P:V.22, J:L.50, O:L.13, O:L.13, O:V.23

2 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)

PL9.6: 15 residues within 4Å: Chain B: F.51, L.52, F.55, A.56, F.59, A.203, L.206 Chain C: I.36, F.40, I.44 Chain I: V.197, W.200, V.204 Ligands: HEM.2, SQD.26 14 PLIP interactions: 9 interactions with chain B, 3 interactions with chain I, 2 interactions with chain C Hydrophobic interactions: B:L.52, B:L.52, B:L.52, B:F.55, B:A.56, B:F.59, B:F.59, B:F.59, B:L.206, I:V.197, I:W.200, I:V.204, C:I.44, C:I.44 PL9.14: 18 residues within 4Å: Chain B: W.200, V.204 Chain I: I.28, F.51, L.52, F.55, A.56, F.59, A.203, R.214 Chain J: W.32, I.36, F.40, P.41, I.44 Ligands: HEM.16, PGV.20, SQD.23 15 PLIP interactions: 1 interactions with chain B, 6 interactions with chain J, 8 interactions with chain I Hydrophobic interactions: B:V.204, J:W.32, J:I.36, J:F.40, J:F.40, J:P.41, J:I.44, I:I.28, I:F.51, I:L.52, I:F.55, I:F.55, I:A.56, I:F.59, I:A.203

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.7: 27 residues within 4Å: Chain B: I.105, F.109, Y.112, W.125, M.130, A.132, V.133, V.136 Chain C: Y.80, P.83, T.84, I.87, M.101, I.104, P.105, L.106, L.108, M.109, V.132, F.133, F.135, G.136, A.139, A.140, L.143 Ligands: PGV.8, LMG.10 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain B, Hydrophobic interactions: C:I.87, C:I.104, C:P.105, C:L.106, C:L.108, C:F.133, C:F.133, C:F.135, C:A.139, C:L.143, B:I.105, B:F.109, B:Y.112, B:Y.112, B:W.125, B:V.133, B:V.136, B:V.136 CLA.17: 28 residues within 4Å: Chain I: I.105, F.109, Y.112, W.125, M.130, A.132, V.133, V.136 Chain J: Y.80, P.83, T.84, I.87, M.101, A.102, I.104, P.105, L.106, L.108, M.109, V.132, F.133, F.135, G.136, A.139, A.140, L.143 Ligands: 2WA.18, PGV.19 19 PLIP interactions: 13 interactions with chain J, 6 interactions with chain I, Hydrophobic interactions: J:I.87, J:A.102, J:P.105, J:L.106, J:L.106, J:L.108, J:L.108, J:F.133, J:F.133, J:F.135, J:A.139, J:A.140, J:L.143, I:I.105, I:F.109, I:Y.112, I:Y.112, I:W.125, I:V.136

2 x HEC: HEME C(Covalent)

HEC.9: 24 residues within 4Å: Chain D: Y.45, P.46, W.48, A.49, I.64, V.65, C.66, C.69, H.70, Q.104, L.114, N.115, V.116, G.117, A.118, V.119, P.162, N.198, G.200, R.201, G.202, I.204, Y.205, P.206 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:Y.45, D:P.46, D:W.48, D:I.64, D:N.115, D:V.119, D:P.162, D:R.201, D:Y.205 Hydrogen bonds: D:Y.45, D:Q.104, D:N.115, D:N.115, D:Y.205, D:Y.205 Salt bridges: D:R.201 pi-Stacking: D:W.48 Metal complexes: D:H.70 HEC.21: 24 residues within 4Å: Chain K: Y.45, P.46, W.48, A.49, I.64, V.65, C.66, C.69, H.70, Q.104, L.114, N.115, V.116, G.117, A.118, V.119, P.162, N.198, G.200, R.201, G.202, I.204, Y.205, P.206 16 PLIP interactions: 16 interactions with chain K, Hydrophobic interactions: K:P.46, K:W.48, K:W.48, K:A.49, K:I.64, K:V.65, K:N.115, K:V.119, K:P.162, K:N.198, K:R.201 Hydrogen bonds: K:Q.104, K:N.115 Salt bridges: K:R.201 pi-Stacking: K:W.48 Metal complexes: K:H.70

1 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.10: 15 residues within 4Å: Chain C: W.79, T.137, A.140, L.141, G.144, A.145, T.148, F.149, L.159 Chain F: E.4, L.7, A.8 Chain G: L.7, L.11 Ligands: CLA.7 12 PLIP interactions: 6 interactions with chain C, 3 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: C:W.79, C:A.140, C:L.141, C:L.141, C:T.148, C:F.149, G:L.7, G:L.11, G:L.11 Hydrogen bonds: F:E.4, F:E.4, F:A.8

2 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.11: 32 residues within 4Å: Chain B: C.50, M.99, M.103 Chain C: A.47, L.50, I.51, L.54 Chain D: Q.82, A.83 Chain E: M.1, G.4, V.5, F.8, I.9 Chain F: M.1, M.6, G.10, I.13, M.14, L.17, L.20 Chain G: L.5, I.9, L.13 Chain H: L.4, T.5, W.8, V.9, V.11, L.12, F.15 Ligands: ECH.5 18 PLIP interactions: 4 interactions with chain G, 5 interactions with chain H, 4 interactions with chain E, 3 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: G:L.5, G:I.9, G:I.9, G:L.13, H:W.8, H:V.11, H:L.12, H:L.12, H:F.15, E:V.5, E:F.8, E:F.8, E:I.9, C:A.47, C:L.50, C:I.51, F:L.17, F:L.20 6PL.25: 27 residues within 4Å: Chain I: M.99, M.103 Chain J: A.47, L.50, L.54 Chain K: Q.82, A.83 Chain M: M.1, V.5, F.8, I.9 Chain N: M.1, M.6, G.10, I.13, M.14, L.17, L.20 Chain O: L.5, I.9 Chain P: L.4, T.5, W.8, V.9, V.11, L.12, F.15 20 PLIP interactions: 5 interactions with chain P, 4 interactions with chain J, 4 interactions with chain O, 2 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: P:W.8, P:V.11, P:L.12, P:L.12, P:F.15, J:A.47, J:L.50, J:L.50, J:L.54, O:L.5, O:I.9, O:I.9, O:I.9, N:I.13, N:L.17, M:V.5, M:F.8, M:F.8, M:F.8, M:I.9

1 x 2WA: (1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol(Non-covalent)

2WA.18: 17 residues within 4Å: Chain I: F.109 Chain J: W.79, Y.82, P.83, T.137, A.138, A.140, L.141, G.144, A.145, T.148, F.149, L.157 Chain N: L.7 Chain O: L.7, L.11 Ligands: CLA.17 12 PLIP interactions: 8 interactions with chain J, 3 interactions with chain O, 1 interactions with chain I Hydrophobic interactions: J:Y.82, J:P.83, J:A.138, J:A.140, J:L.141, J:L.141, J:T.148, J:L.157, O:L.7, O:L.7, O:L.11, I:F.109

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)(Covalent)

FES.22: 10 residues within 4Å: Chain L: C.120, H.122, L.123, G.124, C.125, C.138, C.140, H.141, G.142, S.143 3 PLIP interactions: 3 interactions with chain L, Metal complexes: L:C.120, L:C.138, L:H.141 FES.27: 9 residues within 4Å: Chain Q: C.120, H.122, L.123, C.125, C.138, C.140, H.141, G.142, S.143 4 PLIP interactions: 4 interactions with chain Q, Metal complexes: Q:C.120, Q:H.122, Q:C.138, Q:H.141

2 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.23: 16 residues within 4Å: Chain I: M.1, F.2, S.3, V.6 Chain J: W.32, P.33, L.37, Y.38 Chain K: K.314, I.318 Chain L: R.28, Q.29, N.32, F.36, T.40 Ligands: PL9.14 15 PLIP interactions: 8 interactions with chain L, 3 interactions with chain I, 2 interactions with chain J, 2 interactions with chain K Hydrophobic interactions: L:N.32, L:F.36, L:F.36, L:F.36, L:F.36, I:F.2, I:V.6, J:W.32 Hydrogen bonds: L:N.32, L:N.32, I:S.3, J:W.32 Salt bridges: L:R.28, K:K.314, K:K.314 SQD.26: 16 residues within 4Å: Chain B: M.1, F.2, S.3, V.6 Chain C: W.32, P.33, L.37, Y.38, P.41 Chain D: K.314, I.318 Chain Q: R.28, Q.29, N.32, F.36 Ligands: PL9.6 14 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 1 interactions with chain D, 7 interactions with chain Q Hydrophobic interactions: C:W.32, C:P.41, C:P.41, B:V.6, Q:F.36, Q:F.36, Q:F.36 Hydrogen bonds: B:M.1, B:S.3, Q:Q.29, Q:N.32, Q:N.32 Salt bridges: D:K.314, Q:R.28

1 x LFA: EICOSANE(Non-covalent)

LFA.24: 3 residues within 4Å: Chain M: G.6, G.10, Y.11 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:Y.11, M:Y.11, M:Y.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Proctor, M.S. et al., Cryo-EM structures of the Synechocystis sp. PCC 6803 cytochrome b6f complex with and without the regulatory PetP subunit. Biochem.J. (2022)

Release Date

2022-07-06

Peptides

Uncharacterized protein Cp097, conserved in cyanobacteria: AR
Cytochrome b6: BI
Cytochrome b6-f complex subunit 4: CJ
Cytochrome f: DK
Cytochrome B6: EM
Cytochrome b6-f complex subunit 7: FN
Cytochrome b6-f complex subunit 5: GO
Cytochrome b6-f complex subunit 8: HP
Rieske domain, PetC: LQ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

R
V

B
I

I
A

C
J

J
B

D
K

K
C

E
M

M
E

F
N

N
F

G
O

O
G

H
P

P
H

L
D

Q
L

Membrane

We predict this structure to be a membrane protein.
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Uncharacterized protein Cp097, conserved in cyanobacteria

Cytochrome b6

Cytochrome b6-f complex subunit 4

Cytochrome f

Cytochrome B6

Cytochrome b6-f complex subunit 7

Cytochrome b6-f complex subunit 5

Cytochrome b6-f complex subunit 8

Rieske domain, PetC

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