SMTL ID : 7zxy.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ECH.1: 20 residues within 4Å: Chain A: I.39, F.40, C.42, L.46, M.103, L.106 Chain B: C.43 Chain F: T.18, L.19, L.22 Chain G: L.13, V.16, T.17, A.19, G.20, V.23, L.27 Chain H: S.18, I.19, V.22 16 PLIP interactions: 8 interactions with chain A, 1 interactions with chain H, 4 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: A:I.39, A:I.39, A:I.39, A:F.40, A:F.40, A:L.46, A:L.46, A:L.106, H:V.22, G:L.13, G:V.16, G:V.23, G:L.27, F:T.18, F:L.19, F:L.22 ECH.13: 19 residues within 4Å: Chain I: I.39, F.40, C.42, L.46, M.103, L.106 Chain J: C.43 Chain N: L.19, L.22 Chain O: L.13, V.16, T.17, G.20, V.23, L.27 Chain P: F.15, S.18, I.19, V.22 14 PLIP interactions: 6 interactions with chain I, 4 interactions with chain O, 1 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: I:I.39, I:I.39, I:F.40, I:F.40, I:L.46, I:L.106, O:L.13, O:V.23, O:V.23, O:L.27, N:L.19, P:F.15, P:I.19, P:V.22

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

HEM.2: 24 residues within 4Å: Chain A: F.51, Q.54, F.55, G.58, M.61, T.62, Y.65, V.76, R.90, H.93, R.94, A.97, M.100, T.135, F.138, G.142, L.145, P.146, Y.191, H.194, T.195, P.199 Chain B: E.78 Chain I: F.196 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.51, A:Q.54, A:F.55, A:T.62, A:Y.65, A:A.97, A:T.135, A:F.138, A:F.138, A:F.138, A:L.145, A:L.145, A:Y.191, A:T.195, A:P.199 Salt bridges: A:R.90, A:R.90, A:R.94 Metal complexes: A:H.93, A:H.194 HEM.3: 27 residues within 4Å: Chain A: 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: HEC.4 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:T.47, A:L.48, A:V.108, A:V.108, A:V.111, A:V.111, A:T.124, A:W.125, A:W.125, A:V.129, A:L.131, A:A.132, A:L.206, A:F.210, A:F.210, A:I.213, A:I.218 Hydrogen bonds: A:G.44, A:G.45, A:S.219 Salt bridges: A:H.107, A:R.110, A:R.110, A:R.121 Metal complexes: A:H.107, A:H.209 HEM.15: 22 residues within 4Å: Chain A: F.196 Chain I: Q.54, F.55, G.58, F.59, M.61, T.62, V.76, R.90, H.93, R.94, A.97, M.100, T.135, F.138, G.142, L.145, P.146, Y.191, H.194, P.199 Chain J: E.78 18 PLIP interactions: 16 interactions with chain I, 2 interactions with chain A, Hydrophobic interactions: I:Q.54, I:F.55, I:T.62, I:R.94, I:A.97, I:T.135, I:F.138, I:F.138, I:L.145, I:Y.191, I:P.199, A:F.196, A:F.196 Salt bridges: I:R.90, I:R.90, I:R.94 Metal complexes: I:H.93, I:H.194 HEM.16: 26 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, F.117, T.124, W.125, G.128, V.129, A.132, L.206, H.209, F.210, I.213, G.217, I.218, S.219 Ligands: HEC.17 24 PLIP interactions: 24 interactions with chain I, Hydrophobic interactions: I:T.47, I:L.48, I:V.108, I:V.108, I:V.111, I:V.111, I:T.124, I:W.125, I:W.125, I:W.125, I:V.129, I:A.132, I:L.206, 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.107, I:H.209

4 x HEC: HEME C(Covalent)

HEC.4: 20 residues within 4Å: Chain A: V.37, Y.41, C.42, G.45, L.46, L.48, T.49, F.210, I.213, R.214, G.217, I.218 Chain B: N.25, M.39, F.40, C.43, I.44 Chain H: V.22, R.26 Ligands: HEM.3 17 PLIP interactions: 8 interactions with chain B, 1 interactions with chain H, 8 interactions with chain A, Hydrophobic interactions: B:M.39, B:F.40, B:F.40, B:F.40, B:I.44, B:I.44, H:V.22, A:V.37, A:V.37, A:L.46, A:F.210, A:F.210, A:I.218 Hydrogen bonds: B:N.25, A:I.218 pi-Stacking: B:F.40 Salt bridges: A:R.214 HEC.8: 23 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, T.8, V.21, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:Y.1, C:Y.1, C:Y.1, C:W.4, C:A.5, C:N.71, C:P.118, C:R.157, C:R.157, C:Y.161, C:P.162 Hydrogen bonds: C:Q.60, C:N.71, C:N.71 Salt bridges: C:R.157 pi-Stacking: C:Y.1, C:Y.1, C:W.4 Metal complexes: C:H.26 HEC.17: 18 residues within 4Å: Chain I: V.37, Y.41, C.42, G.45, L.48, T.49, F.210, I.213, R.214, G.217, I.218 Chain J: M.39, F.40, C.43, I.44 Chain P: V.22, R.26 Ligands: HEM.16 15 PLIP interactions: 9 interactions with chain I, 5 interactions with chain J, 1 interactions with chain P, Hydrophobic interactions: I:V.37, I:V.37, I:Y.41, I:L.48, I:F.210, I:F.210, I:I.218, I:I.218, J:M.39, J:F.40, P:V.22 Salt bridges: I:R.214 Hydrogen bonds: J:N.25 pi-Stacking: J:F.40, J:F.40 HEC.22: 23 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, T.8, V.21, C.22, C.25, H.26, Q.60, N.71, V.72, G.73, A.74, V.75, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 17 PLIP interactions: 17 interactions with chain K, Hydrophobic interactions: K:Y.1, K:W.4, K:A.5, K:N.71, K:V.75, K:P.118, K:R.157, K:Y.161, K:Y.161 Hydrogen bonds: K:Q.60, K:N.71, K:N.71, K:Y.161 Salt bridges: K:R.157 pi-Stacking: K:Y.1, K:W.4 Metal complexes: K:H.26

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.5: 23 residues within 4Å: Chain A: I.105, F.109, Y.112, A.132, V.136 Chain B: Y.80, P.83, T.84, M.101, A.102, I.104, P.105, L.106, L.108, V.132, F.133, F.135, G.136, A.139, A.140, L.143 Ligands: PGV.6, PGV.7 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:T.84, B:I.104, B:P.105, B:L.106, B:L.108, B:F.133, B:F.135, B:A.139, B:A.140, B:L.143, A:I.105, A:F.109, A:Y.112, A:Y.112 Hydrogen bonds: B:T.84 CLA.18: 25 residues within 4Å: Chain I: I.105, V.108, F.109, Y.112, W.125, A.132, V.133, V.136 Chain J: Y.80, L.81, P.83, T.84, I.87, A.102, I.104, P.105, L.108, M.109, V.132, F.133, G.136, A.140, L.143 Ligands: PGV.19, PGV.21 19 PLIP interactions: 11 interactions with chain J, 8 interactions with chain I, Hydrophobic interactions: J:L.81, J:T.84, J:I.87, J:A.102, J:I.104, J:I.104, J:L.108, J:F.133, J:F.133, J:L.143, I:V.108, I:F.109, I:Y.112, I:Y.112, I:W.125, I:V.133, I:V.136, I:V.136 Hydrogen bonds: J:T.84

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

PGV.6: 14 residues within 4Å: Chain B: A.103, I.104, G.107, L.108, V.111, I.114, E.115, N.118, R.126, P.127, I.128, A.129, V.132 Ligands: CLA.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.108, B:V.111, B:I.114, B:E.115 Hydrogen bonds: B:N.118, B:N.118, B:I.128, B:A.129 PGV.7: 14 residues within 4Å: Chain B: W.79, Y.82, P.83, A.140, L.141, G.144, A.145, T.148, F.149, L.157 Chain F: L.7 Chain G: L.7, L.11 Ligands: CLA.5 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain G Hydrophobic interactions: B:Y.82, B:P.83, B:L.141, B:A.145, B:L.157, G:L.7, G:L.7, G:L.11, G:L.11 PGV.10: 21 residues within 4Å: Chain A: L.52, I.53, A.56, T.57, N.81, F.85, W.87, L.88, I.92 Chain B: L.48, I.56 Chain C: N.246, T.248, R.249, F.252, L.255, F.256 Chain D: G.29, G.33, A.34, Y.36 17 PLIP interactions: 6 interactions with chain C, 9 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: C:F.252, C:F.252, C:F.256, C:F.256, A:L.52, A:I.53, A:A.56, A:T.57, A:F.85, A:F.85, A:W.87, A:I.92, D:A.34, D:Y.36 Hydrogen bonds: C:N.246, A:W.87 Salt bridges: C:R.249 PGV.14: 23 residues within 4Å: Chain I: A.56, T.57, V.83, N.84, F.85, W.87, L.88, I.89, I.92 Chain J: L.48, A.52, I.56 Chain K: N.246, R.249, F.252, L.255, F.256, G.259 Chain L: T.26, G.33, A.34, Y.36, P.37 19 PLIP interactions: 6 interactions with chain K, 3 interactions with chain L, 7 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: K:F.252, K:F.252, K:L.255, K:F.256, L:T.26, L:Y.36, L:P.37, I:A.56, I:T.57, I:F.85, I:I.89, I:I.92, J:L.48, J:A.52, J:I.56 Hydrogen bonds: K:N.246, I:V.83, I:F.85 Salt bridges: K:R.249 PGV.19: 17 residues within 4Å: Chain J: I.87, G.100, A.103, I.104, G.107, L.108, V.111, I.114, E.115, V.117, N.118, R.126, P.127, I.128, A.129, V.132 Ligands: CLA.18 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:I.87, J:I.104, J:V.111, J:I.114, J:E.115, J:V.132 Hydrogen bonds: J:N.118, J:N.118, J:I.128, J:A.129 PGV.20: 3 residues within 4Å: Chain J: F.124, P.127 Chain O: F.22 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain J Hydrophobic interactions: O:F.22, J:F.124 PGV.21: 16 residues within 4Å: Chain I: F.109 Chain J: W.79, A.140, L.141, G.144, A.145, T.148, F.149, L.157, G.158, L.159, F.160 Chain N: L.7 Chain O: L.7, L.11 Ligands: CLA.18 12 PLIP interactions: 1 interactions with chain I, 7 interactions with chain J, 1 interactions with chain N, 3 interactions with chain O Hydrophobic interactions: I:F.109, J:W.79, J:A.140, J:L.141, J:A.145, J:F.149, J:F.160, J:F.160, N:L.7, O:L.7, O:L.7, O:L.11

2 x LFA: EICOSANE(Non-functional Binders)(Non-covalent)

LFA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LFA.12: 5 residues within 4Å: Chain E: A.2, A.3, G.6, I.7, Y.11 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.7, E:Y.11

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

FES.11: 8 residues within 4Å: Chain D: C.108, H.110, L.111, G.112, C.113, C.126, H.129, S.131 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129 FES.23: 8 residues within 4Å: Chain L: C.108, H.110, L.111, C.113, C.126, C.128, H.129, S.131 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.108, L:H.110, L:C.126, L:H.129

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

Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Cytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit 2: DL
Cytochrome B6: EM
Cytochrome b6-f complex subunit 7: FN
Cytochrome b6-f complex subunit 5: GO
Cytochrome b6-f complex subunit 8: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
I

B
B

J
J

C
C

K
K

D
D

L
L

E
E

M
M

F
F

N
N

G
G

O
O

H
H

P
P

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b6

Cytochrome b6-f complex subunit 4

Cytochrome f

Cytochrome b6-f complex iron-sulfur subunit 2

Cytochrome B6

Cytochrome b6-f complex subunit 7

Cytochrome b6-f complex subunit 5

Cytochrome b6-f complex subunit 8

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