SMTL ID : 6rqf.1

3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules

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: 18 residues within 4Å: Chain A: F.44, Q.47, V.48, G.51, M.54, T.55, V.69, R.83, H.86, R.87, A.90, F.131, G.135, L.138, P.139, H.187, P.192 Chain I: F.189 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain I, Hydrophobic interactions: A:F.44, A:Q.47, A:Q.47, A:V.48, A:T.55, A:A.90, A:F.131, A:F.131, A:F.131, A:F.131, A:L.138, A:P.192, I:F.189, I:F.189 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.187 HEM.2: 24 residues within 4Å: Chain A: Y.34, G.37, G.38, T.40, L.41, M.93, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, L.124, M.199, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:T.40, A:L.41, A:V.101, A:V.104, A:V.104, A:T.117, A:W.118, A:L.124, A:F.203, 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 pi-Cation interactions: A:H.100, A:H.202 Metal complexes: A:H.202 HEM.15: 22 residues within 4Å: Chain A: F.189 Chain I: F.44, Q.47, V.48, G.51, F.52, M.54, T.55, V.69, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.135, L.138, P.139, H.187, P.192 Chain J: E.78 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain I, Hydrophobic interactions: A:F.189, I:F.44, I:Q.47, I:Q.47, I:V.48, I:T.55, I:T.128, I:F.131, I:F.131, I:F.131, I:F.131, I:L.138, I:P.192 Salt bridges: I:R.83, I:R.83, I:R.87 pi-Stacking: I:H.86 Metal complexes: I:H.187 HEM.16: 22 residues within 4Å: Chain I: Y.34, G.37, G.38, T.40, M.97, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, L.124, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.17 21 PLIP interactions: 21 interactions with chain I, Hydrophobic interactions: I:T.40, I:V.101, I:V.101, I:V.104, I:V.104, I:T.117, I:W.118, I:V.122, I:L.124, I:L.124, I:F.203, I:I.206, I:I.211 Hydrogen bonds: I:G.38, I:S.212 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 pi-Cation interactions: I:H.202 Metal complexes: I:H.202

4 x HEC: HEME C(Covalent)

HEC.3: 15 residues within 4Å: Chain A: K.24, V.30, Y.34, C.35, G.38, L.41, F.203, R.207, I.211 Chain B: N.25, F.40, V.43 Chain H: R.26 Ligands: HEM.2, PL9.20 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A, Hydrophobic interactions: B:F.40, B:V.43, A:V.30, A:F.203 pi-Stacking: B:F.40 Hydrogen bonds: A:R.207, A:I.211 Salt bridges: A:K.24, A:R.207 HEC.10: 18 residues within 4Å: Chain C: Y.1, P.2, F.4, C.21, C.24, H.25, Q.59, N.70, V.71, G.72, A.73, V.74, N.153, G.155, R.156, G.157, I.159, Y.160 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Y.1, C:Y.1, C:P.2, C:N.70, C:V.74, C:N.153, C:R.156, C:Y.160 Hydrogen bonds: C:Y.1, C:Q.59, C:N.70 Salt bridges: C:R.156 pi-Stacking: C:Y.1, C:Y.1, C:H.25 Metal complexes: C:H.25 HEC.17: 14 residues within 4Å: Chain I: V.30, Y.34, C.35, G.38, L.41, T.42, F.203, I.206, R.207, G.210, I.211 Chain J: N.25, F.40 Ligands: HEM.16 10 PLIP interactions: 7 interactions with chain I, 3 interactions with chain J, Hydrophobic interactions: I:V.30, I:L.41, I:T.42, I:I.211, I:I.211, J:F.40 Hydrogen bonds: I:I.211, J:N.25 Salt bridges: I:R.207 pi-Stacking: J:F.40 HEC.24: 18 residues within 4Å: Chain K: Y.1, P.2, F.4, C.21, C.24, H.25, Q.59, N.70, V.71, G.72, A.73, P.117, N.153, G.155, R.156, G.157, I.159, Y.160 14 PLIP interactions: 14 interactions with chain K, Hydrophobic interactions: K:Y.1, K:Y.1, K:P.2, K:F.4, K:F.4, K:P.117, K:Y.160 Hydrogen bonds: K:Y.1, K:Q.59, K:N.70 Salt bridges: K:R.156 pi-Stacking: K:Y.1, K:F.4 Metal complexes: K:H.25

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.4: 20 residues within 4Å: Chain A: M.97, I.98, F.102, Y.105, S.130, V.133, L.186 Chain B: Y.80, P.83, V.84, V.104, L.108, V.132, F.133, G.136, V.139 Ligands: PL9.6, LMG.8, PGV.9, SQD.21 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:F.102, A:Y.105, A:V.133, A:L.186, B:L.108, B:L.108, B:V.132, B:F.133, B:F.133, B:V.139 Hydrogen bonds: B:V.84 CLA.18: 19 residues within 4Å: Chain I: I.98, V.101, F.102, Y.105, A.129, V.133, L.186 Chain J: Y.80, P.83, V.84, V.104, L.108, V.132, F.133, G.136, V.139 Ligands: PL9.19, PGV.23, LMG.28 12 PLIP interactions: 8 interactions with chain I, 4 interactions with chain J, Hydrophobic interactions: I:I.98, I:V.101, I:F.102, I:Y.105, I:Y.105, I:A.129, I:V.133, I:L.186, J:L.108, J:L.108, J:F.133, J:V.139

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

BCR.5: 13 residues within 4Å: Chain A: F.33, L.36, L.99 Chain B: V.43 Chain F: T.17, L.18 Chain G: I.16, G.20, L.35 Chain H: F.15, S.18, L.19 Ligands: 6PL.14 12 PLIP interactions: 3 interactions with chain H, 4 interactions with chain A, 2 interactions with chain G, 2 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: H:F.15, H:L.19, H:L.19, A:F.33, A:F.33, A:L.36, A:L.99, G:I.16, G:L.35, F:T.17, F:L.18, B:V.43 BCR.29: 13 residues within 4Å: Chain I: I.32, F.33, I.39, M.96 Chain N: L.18, V.21 Chain O: I.16, G.20, L.35 Chain P: F.15, S.18, L.19 Ligands: 6PL.27 9 PLIP interactions: 4 interactions with chain I, 2 interactions with chain N, 2 interactions with chain P, 1 interactions with chain O Hydrophobic interactions: I:I.32, I:F.33, I:F.33, I:I.39, N:L.18, N:V.21, P:F.15, P:L.19, O:I.16

3 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: 10 residues within 4Å: Chain A: L.116, V.119, V.126, F.198, M.201, L.204, M.205, K.208 Chain I: L.12 Ligands: CLA.4 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:L.116, A:V.119, A:V.126, A:L.204, A:L.204, A:K.208, I:L.12, I:L.12 Hydrogen bonds: A:K.208 PL9.19: 7 residues within 4Å: Chain A: V.48, F.56 Chain D: F.41 Chain I: M.201 Ligands: 6PL.7, CLA.18, PL9.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.56, D:F.41 PL9.20: 17 residues within 4Å: Chain A: F.44, V.48, F.189, P.192, M.199, F.203, R.207 Chain B: L.36, F.40 Chain I: V.48, P.192, L.193, A.196, F.203 Ligands: HEC.3, PL9.19, SQD.25 12 PLIP interactions: 5 interactions with chain A, 5 interactions with chain I, 2 interactions with chain B Hydrophobic interactions: A:F.44, A:V.48, A:F.189, A:P.192, A:F.203, I:V.48, I:P.192, I:L.193, I:A.196, I:F.203, B:L.36, B:F.40

3 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.7: 8 residues within 4Å: Chain A: N.77 Chain D: A.38, F.41, V.42, G.45 Chain I: P.164 Ligands: PGV.11, PL9.19 6 PLIP interactions: 2 interactions with chain I, 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: I:P.164, I:P.164, D:F.41, D:V.42 Hydrogen bonds: A:N.77, A:N.77 6PL.14: 18 residues within 4Å: Chain A: M.92, M.96 Chain B: N.51 Chain E: M.1, T.3, Y.7 Chain F: E.5, R.8, I.9, V.12, M.13, G.15, V.19 Chain G: F.5 Chain H: L.11, M.12, F.15 Ligands: BCR.5 14 PLIP interactions: 1 interactions with chain A, 2 interactions with chain H, 6 interactions with chain F, 1 interactions with chain G, 4 interactions with chain E Hydrophobic interactions: A:M.92, H:L.11, H:F.15, F:I.9, F:V.19, F:V.19, G:F.5, E:Y.7 Salt bridges: F:E.5, F:R.8, F:R.8 Hydrogen bonds: E:M.1, E:T.3, E:T.3 6PL.27: 19 residues within 4Å: Chain I: M.92, M.96 Chain J: C.50, N.51, L.54 Chain M: M.1, T.3, L.4, Y.7 Chain N: R.8, V.12, M.13, G.15, L.16, V.19 Chain P: W.8, L.11, M.12 Ligands: BCR.29 10 PLIP interactions: 3 interactions with chain M, 1 interactions with chain I, 4 interactions with chain N, 1 interactions with chain P, 1 interactions with chain J Hydrophobic interactions: M:L.4, M:Y.7, I:M.92, N:L.16, N:V.19, P:L.11, J:L.54 Hydrogen bonds: M:T.3 Salt bridges: N:R.8, N:R.8

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

LMG.8: 21 residues within 4Å: Chain A: I.98, F.102 Chain B: W.79, F.82, P.83, G.136, T.137, A.140, L.141, G.144, I.145, T.148, L.149 Chain F: N.1, A.3, I.6, F.7 Chain G: F.7, L.11, I.14 Ligands: CLA.4 13 PLIP interactions: 9 interactions with chain B, 1 interactions with chain G, 2 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: B:W.79, B:W.79, B:F.82, B:P.83, B:A.140, B:L.141, B:L.141, B:I.145, G:F.7, F:A.3, A:I.98 Hydrogen bonds: B:T.148, F:N.1 LMG.28: 19 residues within 4Å: Chain I: F.102 Chain J: W.79, F.82, P.83, A.140, L.141, I.145, T.148, L.149, L.159 Chain N: N.1, A.3, I.6, F.7, A.10 Chain O: F.7, L.11, I.14 Ligands: CLA.18 16 PLIP interactions: 1 interactions with chain I, 7 interactions with chain J, 3 interactions with chain O, 5 interactions with chain N Hydrophobic interactions: I:F.102, J:W.79, J:F.82, J:A.140, J:L.141, J:I.145, J:I.145, J:T.148, O:F.7, O:L.11, O:I.14, N:I.6, N:F.7, N:A.10 Hydrogen bonds: N:N.1, N:N.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.9: 10 residues within 4Å: Chain B: S.103, G.107, L.114, E.115, N.118, R.126, P.127, V.128, A.129 Ligands: CLA.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.114, B:E.115 Hydrogen bonds: B:N.118, B:V.128, B:A.129 PGV.11: 12 residues within 4Å: Chain A: A.49, T.50, N.77, F.78, W.80, L.81 Chain C: D.247, L.249, R.250 Chain D: Y.32, P.36 Ligands: 6PL.7 8 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:T.50, A:N.77, A:F.78, A:F.78, A:L.81, D:P.36 Hydrogen bonds: A:F.78 Salt bridges: C:R.250 PGV.22: 9 residues within 4Å: Chain I: E.75, N.77, F.78, W.80, L.81 Chain J: V.52 Chain L: Y.32, M.33, L.35 10 PLIP interactions: 5 interactions with chain L, 2 interactions with chain J, 3 interactions with chain I Hydrophobic interactions: L:Y.32, L:Y.32, L:Y.32, L:M.33, L:L.35, J:V.52, J:V.52, I:L.81 Hydrogen bonds: I:E.75, I:F.78 PGV.23: 12 residues within 4Å: Chain J: S.103, G.107, L.108, V.111, L.114, E.115, N.118, R.125, R.126, V.128, A.129 Ligands: CLA.18 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:L.114 Hydrogen bonds: J:N.118, J:A.129

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

FES.12: 10 residues within 4Å: Chain D: C.107, H.109, L.110, G.111, C.112, C.125, C.127, H.128, G.129, S.130 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.107, D:H.109, D:C.125, D:H.128 FES.26: 9 residues within 4Å: Chain L: C.107, H.109, L.110, C.112, C.125, C.127, H.128, G.129, S.130 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.107, L:H.109, L:C.125, L:H.128

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

SQD.13: 9 residues within 4Å: Chain B: W.32, P.41 Chain C: K.271, F.275 Chain D: R.15, N.19, L.22, L.23, L.26 7 PLIP interactions: 1 interactions with chain B, 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: B:P.41, D:L.22, D:L.23 Hydrogen bonds: D:N.19, D:N.19 Salt bridges: D:R.15, C:K.271 SQD.21: 9 residues within 4Å: Chain A: L.168, L.169, L.186 Chain I: F.56 Chain L: A.38, S.39, F.41, V.42 Ligands: CLA.4 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: L:A.38, A:L.168 SQD.25: 12 residues within 4Å: Chain J: W.32, P.33, L.37, P.41 Chain K: K.271, F.275 Chain L: R.15, N.19, L.22, L.23, L.26 Ligands: PL9.20 8 PLIP interactions: 4 interactions with chain J, 3 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: J:L.37, J:P.41, J:P.41, L:L.22 Hydrogen bonds: J:W.32, L:N.19 Salt bridges: L:R.15, K:K.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malone, L.A. et al., Cryo-EM structure of the spinach cytochrome b6f complex at 3.6 angstrom resolution. Nature (2019)

Release Date

2019-11-13

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
I

I
A

B
J

J
B

C
K

K
C

D
L

L
D

E
M

M
E

F
N

N
F

G
O

O
G

H
P

P
H

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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