SMTL ID : 7qrm.1

Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 13 residues within 4Å: Chain A: Q.47, G.51, F.52, M.54, R.83, H.86, R.87, A.90, F.131, G.135, L.138, P.139, H.187 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:Q.47, A:A.90, A:F.131, A:F.131, A:F.131, A:L.138 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEM.2: 21 residues within 4Å: Chain A: Y.34, G.37, G.38, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, M.199, H.202, F.203, I.206, G.210, I.211, S.212 Ligands: HEC.3 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:V.104, A:T.117, A:W.118, A:F.203 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.20: 12 residues within 4Å: Chain I: Q.47, G.51, M.54, R.83, H.86, R.87, A.90, F.131, G.135, L.138, P.139, H.187 11 PLIP interactions: 11 interactions with chain I, Hydrophobic interactions: I:Q.47, I:A.90, I:F.131, I:F.131, I:F.131, I:L.138 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEM.21: 18 residues within 4Å: Chain I: Y.34, G.37, M.97, H.100, V.101, R.103, V.104, G.109, T.117, W.118, G.121, V.122, L.124, H.202, I.206, I.211, S.212 Ligands: HEC.22 14 PLIP interactions: 14 interactions with chain I, Hydrophobic interactions: I:V.101, I:V.104, I:T.117, I:W.118, I:V.122, I:L.124, I:I.206 Hydrogen bonds: I:S.212 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202

4 x HEC: HEME C(Non-covalent)(Covalent)

HEC.3: 11 residues within 4Å: Chain A: Y.34, C.35, G.38, L.41, T.42, R.207, I.211 Chain B: F.40, I.44 Ligands: HEM.2, PL9.19 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:L.41, A:I.211, B:I.44 Hydrogen bonds: A:I.211 Salt bridges: A:R.207 pi-Stacking: B:F.40 HEC.12: 16 residues within 4Å: Chain C: Y.36, F.39, A.40, C.56, C.59, H.60, Q.94, N.105, V.106, G.107, N.188, G.190, R.191, G.192, I.194, Y.195 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:Y.36, C:F.39, C:A.40, C:N.105, C:N.188, C:R.191, C:Y.195 Hydrogen bonds: C:Q.94, C:N.105, C:Y.195 Salt bridges: C:R.191 Metal complexes: C:H.60 HEC.22: 14 residues within 4Å: Chain I: V.30, N.31, Y.34, C.35, G.38, L.41, I.206, R.207, I.211 Chain J: I.39, F.40, V.43 Ligands: PL9.19, HEM.21 10 PLIP interactions: 5 interactions with chain J, 5 interactions with chain I, Hydrophobic interactions: J:I.39, J:F.40, J:F.40, J:V.43, I:V.30, I:L.41, I:I.206 pi-Stacking: J:F.40 Hydrogen bonds: I:I.211 Salt bridges: I:R.207 HEC.32: 19 residues within 4Å: Chain K: Y.36, P.37, F.39, A.40, C.56, C.59, H.60, Q.94, L.104, N.105, V.106, G.107, A.108, N.188, G.190, R.191, G.192, I.194, Y.195 7 PLIP interactions: 7 interactions with chain K, Hydrophobic interactions: K:Y.36, K:A.40 Hydrogen bonds: K:Q.94, K:N.105 Salt bridges: K:R.191 pi-Stacking: K:Y.36 Metal complexes: K:H.60

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.4: 18 residues within 4Å: Chain A: I.98, F.102, Y.105, G.125, S.130, V.133 Chain B: Y.80, P.83, V.84, M.101, L.108, F.133, G.136, V.139 Ligands: PL9.5, PL9.9, UMQ.10, UMQ.11 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:F.102, A:Y.105, A:Y.105, A:V.133, B:L.108, B:L.108, B:F.133, B:V.139 CLA.27: 13 residues within 4Å: Chain I: F.102, S.130 Chain J: Y.80, P.83, V.84, V.132, F.133, G.136, V.139 Ligands: PL9.28, PL9.29, UMQ.30, UMQ.31 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I, Hydrophobic interactions: J:F.133, J:V.139, I:F.102

7 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)

PL9.5: 16 residues within 4Å: Chain A: V.123, V.126, S.130, V.133, T.134, A.147, I.150, V.151, L.169 Chain B: F.81, V.84, F.85, M.101, A.102, P.105 Ligands: CLA.4 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.123, A:V.126, A:V.133, A:T.134, A:A.147, A:I.150, A:V.151, A:V.151, A:L.169, B:F.81, B:F.81, B:V.84, B:F.85, B:F.85, B:P.105 PL9.9: 21 residues within 4Å: Chain B: L.73, E.74, I.75, W.79, F.82, R.89, T.137, A.140, L.141, G.144, I.145, T.148 Chain F: A.3 Chain G: I.2, F.7, V.10, L.11 Chain L: P.177, C.178, H.179 Ligands: CLA.4 14 PLIP interactions: 5 interactions with chain G, 8 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: G:I.2, G:F.7, G:V.10, G:L.11, G:L.11, B:W.79, B:F.82, B:A.140, B:L.141, B:I.145, B:T.148, F:A.3 Hydrogen bonds: B:I.75, B:R.89 PL9.14: 17 residues within 4Å: Chain A: V.48, F.52, N.77, F.78, W.80, L.81 Chain B: V.52, V.56 Chain C: L.284, R.285, G.288 Chain D: Y.83, M.84, L.85, Y.88 Chain I: L.193 Ligands: PGT.16 13 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 6 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: D:M.84, D:L.85, D:Y.88, D:Y.88, B:V.52, B:V.56, A:V.48, A:F.52, A:F.52, A:N.77, I:L.193 Hydrogen bonds: A:F.78 pi-Stacking: A:F.78 PL9.19: 26 residues within 4Å: Chain A: L.41, F.44, L.45, V.48, F.189, P.192, L.193, A.196, M.199, L.200, F.203 Chain B: I.44 Chain I: L.41, F.44, L.45, V.48, F.189, P.192, L.193, A.196, M.199, F.203 Chain J: L.36, F.40 Ligands: HEC.3, HEC.22 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: A:F.44, A:F.189, A:P.192, J:F.40, I:F.189, I:P.192 PL9.26: 16 residues within 4Å: Chain A: F.189, V.190 Chain I: V.46, F.52, N.77, F.78, W.80, L.81 Chain J: V.52 Chain K: R.285 Chain L: Y.83, M.84, L.85, Y.88 Ligands: SQD.33, PGT.34 10 PLIP interactions: 5 interactions with chain I, 1 interactions with chain J, 2 interactions with chain L, 2 interactions with chain A Hydrophobic interactions: I:V.46, I:F.52, I:L.81, I:L.81, J:V.52, L:M.84, L:L.85, A:F.189, A:V.190 pi-Stacking: I:F.78 PL9.28: 20 residues within 4Å: Chain I: V.123, V.126, S.130, T.134, W.146, A.147, I.150, V.151, T.152, V.154, L.169 Chain J: I.75, P.77, F.81, F.85, M.101, A.106, L.109 Ligands: PGT.8, CLA.27 16 PLIP interactions: 10 interactions with chain I, 6 interactions with chain J Hydrophobic interactions: I:V.123, I:V.126, I:T.134, I:I.150, I:V.151, I:V.151, I:V.151, I:V.151, I:V.154, I:L.169, J:I.75, J:P.77, J:F.81, J:F.85, J:F.85, J:A.106 PL9.29: 19 residues within 4Å: Chain D: C.178, H.179 Chain J: L.73, E.74, I.75, W.79, F.82, R.89, T.137, I.145, T.148, L.149 Chain K: Q.273, G.274 Chain N: A.3 Chain O: I.2, F.7, L.11 Ligands: CLA.27 13 PLIP interactions: 9 interactions with chain J, 3 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: J:L.73, J:E.74, J:W.79, J:W.79, J:F.82, J:T.137, J:I.145, J:L.149, O:I.2, O:F.7, O:L.11, N:A.3 Hydrogen bonds: J:I.75

10 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.6: 7 residues within 4Å: Chain A: S.2, Y.5, I.14, Q.15, I.17, A.18 Ligands: UMQ.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.14 Hydrogen bonds: A:Q.15, A:Q.15 UMQ.7: 9 residues within 4Å: Chain A: Q.15, A.18, I.21, T.22 Chain B: W.32 Chain C: N.319, F.320 Ligands: UMQ.6, SQD.13 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:F.320 Hydrophobic interactions: A:I.21, B:W.32 UMQ.10: 15 residues within 4Å: Chain B: S.103, V.104, G.107, L.108, T.110, V.111, L.114, E.115, V.117, N.118, P.127, V.128, A.129, V.132 Ligands: CLA.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.108, B:L.114 Hydrogen bonds: B:N.118 UMQ.11: 13 residues within 4Å: Chain B: I.87, T.90, V.91, L.100, S.103, V.104, V.139, L.143, I.151, S.154, L.155 Chain L: P.193 Ligands: CLA.4 No protein-ligand interaction detected (PLIP) UMQ.18: 20 residues within 4Å: Chain A: M.92 Chain B: C.50, L.54 Chain C: Q.72, A.73 Chain E: M.1, T.3 Chain F: R.8, I.9, M.13, L.16 Chain G: F.5, I.9 Chain H: D.2, V.4, S.5, W.8, L.11, M.12, F.15 10 PLIP interactions: 2 interactions with chain F, 2 interactions with chain C, 1 interactions with chain E, 5 interactions with chain H Hydrogen bonds: F:R.8, C:Q.72, C:A.73, E:T.3, H:D.2, H:S.5, H:S.5 Salt bridges: F:R.8 Hydrophobic interactions: H:L.11, H:F.15 UMQ.23: 9 residues within 4Å: Chain I: Q.15, I.17, A.18, D.19, I.21, T.22 Chain J: W.32 Ligands: UMQ.24, SQD.33 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:I.21, J:W.32, J:W.32 Hydrogen bonds: I:Q.15, I:T.22 UMQ.24: 6 residues within 4Å: Chain I: Y.5, I.14, Q.15, I.17, A.18 Ligands: UMQ.23 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.15 UMQ.30: 12 residues within 4Å: Chain J: I.87, T.90, V.91, P.92, L.100, S.103, V.104, L.143, I.151, S.154, L.155 Ligands: CLA.27 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:T.90, J:S.154 UMQ.31: 12 residues within 4Å: Chain J: V.104, G.107, L.108, T.110, V.111, L.114, E.115, N.118, R.126, V.128, V.132 Ligands: CLA.27 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:L.108, J:L.114 Hydrogen bonds: J:L.114, J:A.129 UMQ.37: 23 residues within 4Å: Chain I: M.92 Chain J: C.50, L.54 Chain K: Q.72, A.73 Chain M: M.1, T.3 Chain N: E.5, R.8, I.9, V.12, M.13, L.16 Chain O: F.5, I.9, L.13 Chain P: D.2, V.4, S.5, W.8, L.11, M.12, F.15 9 PLIP interactions: 3 interactions with chain N, 2 interactions with chain M, 1 interactions with chain P, 3 interactions with chain K Hydrogen bonds: N:E.5, N:R.8, M:T.3, M:T.3, P:D.2, K:Q.72, K:A.73, K:A.73 Salt bridges: N:R.8

4 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.8: 13 residues within 4Å: Chain A: K.3, V.4, W.7, F.8, E.10 Chain I: L.116, V.119, V.123 Chain J: A.106, L.109, T.110, F.113 Ligands: PL9.28 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: A:V.4, A:W.7, A:W.7, J:L.109, J:F.113, J:F.113, J:F.113 Hydrogen bonds: A:E.10 Salt bridges: A:K.3 PGT.16: 7 residues within 4Å: Chain D: A.89, S.90, F.92, V.93 Chain I: L.168, L.186 Ligands: PL9.14 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain I Hydrophobic interactions: D:F.92, D:F.92, D:F.92, D:V.93, I:L.168, I:L.186 PGT.25: 10 residues within 4Å: Chain A: L.116, V.119, F.198 Chain B: A.106, L.109, T.110, F.113 Chain I: K.3, W.7, F.8 10 PLIP interactions: 2 interactions with chain A, 4 interactions with chain I, 4 interactions with chain B Hydrophobic interactions: A:L.116, A:V.119, I:W.7, I:W.7, B:T.110, B:F.113, B:F.113, B:F.113 Hydrogen bonds: I:K.3 Salt bridges: I:K.3 PGT.34: 7 residues within 4Å: Chain I: F.56, N.77 Chain L: L.86, A.89, S.90, F.92 Ligands: PL9.26 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain I Hydrophobic interactions: L:L.86, L:F.92, L:F.92, I:F.56 Hydrogen bonds: I:N.77

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

SQD.13: 11 residues within 4Å: Chain B: W.32, L.37, P.41, I.44 Chain C: K.306, F.310 Chain D: R.66, N.70, L.77, M.84 Ligands: UMQ.7 8 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:L.77, B:L.37, B:P.41, B:I.44 Hydrogen bonds: D:N.70, B:W.32 Salt bridges: D:R.66, C:K.306 SQD.33: 11 residues within 4Å: Chain J: W.32, P.41 Chain K: K.306, F.310 Chain L: R.66, N.70, L.73, L.74, L.77 Ligands: UMQ.23, PL9.26 8 PLIP interactions: 5 interactions with chain L, 1 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: L:L.73, L:L.74, L:L.77, J:P.41 Hydrogen bonds: L:N.70, J:W.32 Salt bridges: L:R.66, K:K.306

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

FES.15: 10 residues within 4Å: Chain D: C.158, H.160, L.161, G.162, C.163, C.176, C.178, H.179, G.180, S.181 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.158, D:H.160, D:C.176, D:H.179 FES.35: 9 residues within 4Å: Chain L: C.158, H.160, L.161, G.162, C.163, C.176, H.179, G.180, S.181 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.158, L:H.160, L:C.176, L:H.179

2 x BCR: BETA-CAROTENE(Non-covalent)

BCR.17: 9 residues within 4Å: Chain A: I.32 Chain F: T.17 Chain G: L.13, I.16, G.20, L.27 Chain H: F.15, S.18, L.19 7 PLIP interactions: 1 interactions with chain F, 3 interactions with chain G, 2 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: F:T.17, G:L.13, G:I.16, G:L.27, H:F.15, H:L.19, A:I.32 BCR.36: 11 residues within 4Å: Chain I: I.32, F.33, M.96 Chain J: V.43 Chain N: T.17 Chain O: I.16, G.20, L.27 Chain P: F.15, S.18, L.19 7 PLIP interactions: 1 interactions with chain O, 2 interactions with chain I, 2 interactions with chain P, 1 interactions with chain N, 1 interactions with chain J Hydrophobic interactions: O:L.27, I:I.32, I:F.33, P:F.15, P:L.19, N:T.17, J:V.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sarewicz, M. et al., High-resolution cryo-EM structures of plant cytochrome b 6 f at work. Sci Adv (2023)

Release Date

2023-01-25

Peptides

Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Cytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit, chloroplastic: DL
Cytochrome b6-f complex subunit 6: 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, chloroplastic

Cytochrome b6-f complex subunit 6

Cytochrome b6-f complex subunit 7

Cytochrome b6-f complex subunit 5

Cytochrome b6-f complex subunit 8

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