SMTL ID : 9es8.1

Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 12 residues within 4Å: Chain A: 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 A, Hydrophobic interactions: A:A.90, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138 Hydrogen bonds: A:R.87 Salt bridges: A:R.83, A:R.83 Metal complexes: A:H.86, A:H.187 HEM.2: 19 residues within 4Å: Chain A: Y.34, G.37, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.3 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:V.101, A:V.104, A:T.117, A:W.118, A:V.122, A:F.203, A:I.206 Hydrogen bonds: A:G.37, A:S.212 Water bridges: A:L.36, A:G.38 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.12: 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:A.90, I:F.131, I:F.131, I:F.131, I:F.131, I:L.138 Hydrogen bonds: I:R.87 Salt bridges: I:R.83, I:R.83 Metal complexes: I:H.86, I:H.187 HEM.13: 19 residues within 4Å: Chain I: Y.34, G.37, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.14 17 PLIP interactions: 17 interactions with chain I, Hydrophobic interactions: I:V.101, I:V.104, I:T.117, I:W.118, I:V.122, I:F.203, I:I.206 Hydrogen bonds: I:G.37, I:S.212 Water bridges: I:L.36, I:G.38 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(Covalent)

HEC.3: 12 residues within 4Å: Chain A: Y.34, C.35, G.38, T.42, R.207, G.210, I.211 Chain B: I.39, F.40, I.44 Ligands: HEM.2, 01.4 8 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B, 1 Ligand-Water interactions, Hydrogen bonds: A:I.211 Salt bridges: A:R.207 Hydrophobic interactions: B:I.39, B:F.40, B:F.40, B:F.40, B:I.44 Metal complexes: H2O.1 HEC.8: 17 residues within 4Å: Chain C: Y.36, P.37, F.39, C.56, C.59, H.60, Q.94, L.104, N.105, V.106, G.107, N.188, G.190, R.191, G.192, I.194, Y.195 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:Y.36, C:F.39, C:N.105, C:R.191 Hydrogen bonds: C:Q.94, C:N.105, C:G.190, C:Y.195 Salt bridges: C:R.191 pi-Stacking: C:F.39 Metal complexes: C:H.60 HEC.14: 12 residues within 4Å: Chain I: Y.34, C.35, G.38, T.42, R.207, G.210, I.211 Chain J: I.39, F.40, I.44 Ligands: HEM.13, 01.15 8 PLIP interactions: 2 interactions with chain I, 5 interactions with chain J, 1 Ligand-Water interactions, Hydrogen bonds: I:I.211 Salt bridges: I:R.207 Hydrophobic interactions: J:I.39, J:F.40, J:F.40, J:F.40, J:I.44 Metal complexes: H2O.5 HEC.19: 17 residues within 4Å: Chain K: Y.36, P.37, F.39, C.56, C.59, H.60, Q.94, L.104, N.105, V.106, G.107, N.188, G.190, R.191, G.192, I.194, Y.195 11 PLIP interactions: 11 interactions with chain K, Hydrophobic interactions: K:Y.36, K:F.39, K:N.105, K:R.191 Hydrogen bonds: K:Q.94, K:N.105, K:G.190, K:Y.195 Salt bridges: K:R.191 pi-Stacking: K:F.39 Metal complexes: K:H.60

2 x 01: Decylplastoquinone

01.4: 7 residues within 4Å: Chain A: K.24, Y.25, V.26, R.207 Chain B: L.36, F.40 Ligands: HEC.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.36, B:F.40, A:K.24, A:K.24 Hydrogen bonds: A:R.207 01.15: 7 residues within 4Å: Chain I: K.24, Y.25, V.26, R.207 Chain J: L.36, F.40 Ligands: HEC.14 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:K.24, I:K.24, J:L.36, J:F.40 Hydrogen bonds: I:R.207

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

LMG.5: 7 residues within 4Å: Chain A: S.2, Y.5, F.8, Q.15, I.17 Ligands: UMQ.7, SQD.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.5, A:F.8, A:I.17 Hydrogen bonds: A:Q.15 LMG.16: 7 residues within 4Å: Chain I: S.2, Y.5, F.8, Q.15, I.17 Ligands: UMQ.18, SQD.20 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:Y.5, I:F.8, I:I.17 Hydrogen bonds: I:Q.15

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.6: 14 residues within 4Å: Chain A: M.97, F.102, V.126, S.130, V.133 Chain B: Y.80, P.83, V.84, M.101, L.108, V.132, F.133, G.136, V.139 9 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.108, B:V.132, B:F.133, B:V.139, A:F.102, A:V.126, A:V.133 Water bridges: B:V.84 Metal complexes: H2O.2 CLA.17: 14 residues within 4Å: Chain I: M.97, F.102, V.126, S.130, V.133 Chain J: Y.80, P.83, V.84, M.101, L.108, V.132, F.133, G.136, V.139 9 PLIP interactions: 5 interactions with chain J, 3 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:L.108, J:V.132, J:F.133, J:V.139, I:F.102, I:V.126, I:V.133 Water bridges: J:V.84 Metal complexes: H2O.6

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

UMQ.7: 9 residues within 4Å: Chain A: Q.15, A.18, D.19, I.21, T.22 Chain B: W.32 Chain C: N.319 Ligands: LMG.5, SQD.9 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.21, A:T.22, B:W.32, B:W.32 Hydrogen bonds: A:Q.15, A:D.19, A:T.22 UMQ.11: 13 residues within 4Å: Chain C: Q.72, A.73 Chain E: M.1, T.3 Chain F: R.101 Chain G: F.5 Chain H: D.2, V.4, S.5, W.8, L.11, M.12, F.15 8 PLIP interactions: 3 interactions with chain H, 3 interactions with chain C, 1 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: H:L.11, H:F.15 Hydrogen bonds: H:D.2, C:Q.72, C:A.73, C:A.73, E:T.3 Salt bridges: F:R.101 UMQ.18: 9 residues within 4Å: Chain I: Q.15, A.18, D.19, I.21, T.22 Chain J: W.32 Chain K: N.319 Ligands: LMG.16, SQD.20 7 PLIP interactions: 2 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:W.32, J:W.32, I:I.21, I:T.22 Hydrogen bonds: I:Q.15, I:D.19, I:T.22 UMQ.22: 13 residues within 4Å: Chain K: Q.72, A.73 Chain M: M.1, T.3 Chain N: M.106 Chain O: F.5 Chain P: D.2, V.4, S.5, W.8, L.11, M.12, F.15 8 PLIP interactions: 3 interactions with chain P, 1 interactions with chain M, 3 interactions with chain K, 1 interactions with chain N Hydrophobic interactions: P:L.11, P:F.15 Hydrogen bonds: P:D.2, M:T.3, K:Q.72, K:A.73, K:A.73 Salt bridges: N:R.101

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

SQD.9: 12 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.73, L.77 Ligands: LMG.5, UMQ.7 11 PLIP interactions: 6 interactions with chain B, 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: B:L.37, B:P.41, B:I.44, D:L.73, D:L.77 Hydrogen bonds: B:W.32, D:N.70 Water bridges: B:Y.38, B:Y.38 Salt bridges: D:R.66, C:K.306 SQD.20: 12 residues within 4Å: Chain J: W.32, L.37, P.41, I.44 Chain K: K.306, F.310 Chain L: R.66, N.70, L.73, L.77 Ligands: LMG.16, UMQ.18 11 PLIP interactions: 6 interactions with chain J, 1 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: J:L.37, J:P.41, J:I.44, L:L.73, L:L.77 Hydrogen bonds: J:W.32, L:N.70 Water bridges: J:Y.38, J:Y.38 Salt bridges: K:K.306, L:R.66

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

FES.10: 8 residues within 4Å: Chain D: C.158, H.160, L.161, C.163, C.176, C.178, H.179, 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.21: 8 residues within 4Å: Chain L: C.158, H.160, L.161, C.163, C.176, C.178, H.179, 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.23: 7 residues within 4Å: Chain A: I.39, M.96 Chain F: T.110 Chain G: G.20 Chain H: F.15, L.19 Chain Q: L.39 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H, 1 interactions with chain F, 1 interactions with chain Q Hydrophobic interactions: A:I.39, H:F.15, F:T.110, Q:L.39 BCR.24: 7 residues within 4Å: Chain I: I.39, M.96 Chain N: T.110 Chain O: G.20 Chain P: F.15, L.19 Chain R: L.39 4 PLIP interactions: 1 interactions with chain N, 1 interactions with chain P, 1 interactions with chain I, 1 interactions with chain R Hydrophobic interactions: N:T.110, P:F.15, I:I.39, R:L.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pintscher, S. et al., Molecular basis of plastoquinone reduction in plant cytochrome b 6 f. Nat.Plants (2024)

Release Date

2024-10-16

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
Thylakoid soluble phosphoprotein: QR

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

Q
Q

R
R

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

Thylakoid soluble phosphoprotein

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