SMTL ID : 7zyv.1

Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution

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: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: 20 residues within 4Å: Chain A: Y.34, G.37, G.38, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, M.199, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.3 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.101, A:V.104, A:T.117, A:W.118, A:V.122, 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.17: 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.18: 20 residues within 4Å: Chain I: Y.34, G.37, G.38, H.100, V.101, R.103, V.104, G.109, R.114, T.117, W.118, G.121, V.122, M.199, H.202, F.203, I.206, I.211, S.212 Ligands: HEC.19 15 PLIP interactions: 15 interactions with chain I, Hydrophobic interactions: I:V.101, I:V.104, I:T.117, I:W.118, I:V.122, I:F.203 Hydrogen bonds: I:G.37, I:G.38, 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(Covalent)

HEC.3: 12 residues within 4Å: Chain A: N.31, Y.34, C.35, G.38, T.42, I.206, R.207, I.211 Chain B: I.39, F.40, V.43 Ligands: HEM.2 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B, Hydrogen bonds: A:I.211 Salt bridges: A:R.207 Hydrophobic interactions: B:I.39, B:F.40, B:V.43 pi-Stacking: B:F.40 HEC.12: 19 residues within 4Å: Chain C: 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 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:Y.36, C:F.39, C:N.105 Hydrogen bonds: C:Y.36, C:Q.94, C:N.105, C:Y.195 Salt bridges: C:R.191 Metal complexes: C:H.60 HEC.19: 12 residues within 4Å: Chain I: N.31, Y.34, C.35, G.38, T.42, I.206, R.207, I.211 Chain J: I.39, F.40, V.43 Ligands: HEM.18 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain I, Hydrophobic interactions: J:I.39, J:F.40, J:F.40, J:V.43 pi-Stacking: J:F.40 Hydrogen bonds: I:I.211 Salt bridges: I:R.207 HEC.27: 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 9 PLIP interactions: 9 interactions with chain K, Hydrophobic interactions: K:Y.36, K:F.39, K:N.105 Hydrogen bonds: K:Y.36, K:Q.94, K:N.105, K:Y.195 Salt bridges: K:R.191 Metal complexes: K:H.60

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.4: 15 residues within 4Å: Chain A: M.97, F.102, Y.105, S.130 Chain B: Y.80, P.83, M.101, L.108, F.133, G.136, V.139 Ligands: PL9.8, PL9.9, UMQ.10, UMQ.11 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:F.133, B:V.139, A:F.102, A:Y.105, A:Y.105 CLA.20: 15 residues within 4Å: Chain I: M.97, F.102, Y.105, S.130 Chain J: Y.80, P.83, M.101, L.108, F.133, G.136, V.139 Ligands: PL9.23, PL9.24, UMQ.25, UMQ.26 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J, Hydrophobic interactions: I:F.102, I:Y.105, I:Y.105, J:F.133, J:V.139

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

UMQ.5: 7 residues within 4Å: Chain A: S.2, Y.5, I.14, Q.15, I.17, A.18 Ligands: UMQ.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.15 UMQ.6: 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: UMQ.5, SQD.13 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:W.32, B:W.32 Hydrogen bonds: A:D.19, A:T.22, C:N.319 UMQ.10: 16 residues within 4Å: Chain B: S.103, V.104, G.107, L.108, V.111, L.114, E.115, V.117, N.118, R.126, P.127, V.128, A.129, V.132 Ligands: CLA.4, UMQ.11 No protein-ligand interaction detected (PLIP) UMQ.11: 14 residues within 4Å: Chain B: I.87, T.90, V.91, P.92, L.100, S.103, V.104, L.143, I.151, D.152, S.154, L.155 Ligands: CLA.4, UMQ.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.87 Hydrogen bonds: B:S.154 UMQ.16: 22 residues within 4Å: Chain A: M.92 Chain B: C.50, L.54 Chain C: P.71, Q.72, A.73 Chain E: M.1, T.3 Chain F: R.101, I.102, V.105, M.106, L.109 Chain G: F.5, I.9 Chain H: D.2, V.4, S.5, W.8, L.11, M.12, F.15 11 PLIP interactions: 6 interactions with chain H, 3 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: H:F.15 Hydrogen bonds: H:D.2, H:D.2, H:D.2, H:S.5, H:S.5, C:Q.72, C:A.73, C:A.73, F:R.101 Salt bridges: F:R.101 UMQ.21: 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: UMQ.22, SQD.29 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:W.32, J:W.32 Hydrogen bonds: I:D.19, I:T.22 UMQ.22: 6 residues within 4Å: Chain I: Y.5, I.14, Q.15, I.17, A.18 Ligands: UMQ.21 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.15 UMQ.25: 11 residues within 4Å: Chain J: I.87, T.90, V.91, L.100, S.103, V.104, L.143, I.151, S.154, L.155 Ligands: CLA.20 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.154 UMQ.26: 15 residues within 4Å: Chain J: S.103, V.104, G.107, L.108, V.111, L.114, E.115, V.117, N.118, R.126, P.127, V.128, A.129, V.132 Ligands: CLA.20 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:L.114 UMQ.32: 21 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: R.101, I.102, V.105, M.106 Chain O: F.5, I.9, L.13 Chain P: D.2, V.4, S.5, W.8, L.11, M.12, F.15 10 PLIP interactions: 5 interactions with chain P, 3 interactions with chain K, 1 interactions with chain N, 1 interactions with chain M Hydrogen bonds: P:D.2, P:D.2, P:D.2, P:S.5, P:S.5, K:Q.72, K:A.73, K:A.73, M:T.3 Salt bridges: N:R.101

6 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)

PL9.7: 12 residues within 4Å: Chain A: L.45, F.78, W.80, L.81 Chain B: V.56 Chain C: L.284, R.285, F.292 Chain D: Y.83, M.84 Ligands: SQD.13, PL9.23 7 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:L.45, A:L.81, D:Y.83, D:M.84, B:V.56, C:F.292 Hydrogen bonds: A:F.78 PL9.8: 17 residues within 4Å: Chain A: S.130, V.133, T.134, A.147, I.150, V.151 Chain B: I.75, P.77, F.81, F.85, L.88, M.101 Chain I: V.48, F.52 Chain L: Y.88 Ligands: CLA.4, PL9.28 12 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:V.133, A:T.134, A:I.150, A:I.150, B:I.75, B:P.77, B:F.81, B:F.85, B:F.85, B:L.88, I:V.48, I:F.52 PL9.9: 18 residues within 4Å: Chain A: F.102 Chain B: P.72, L.73, E.74, I.75, W.79, F.82, R.89, T.137, L.141, G.144, T.148 Chain F: A.95 Chain G: V.10, L.11 Chain L: C.178, H.179 Ligands: CLA.4 13 PLIP interactions: 2 interactions with chain G, 1 interactions with chain F, 1 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: G:V.10, G:L.11, F:A.95, A:F.102, B:E.74, B:I.75, B:W.79, B:F.82, B:T.137, B:L.141, B:T.148 Hydrogen bonds: B:I.75, B:R.89 PL9.23: 17 residues within 4Å: Chain A: V.48, F.52 Chain I: S.130, V.133, I.150, V.151, F.183, V.190, L.193 Chain J: I.75, P.77, F.81, F.85, L.88, M.101 Ligands: PL9.7, CLA.20 12 PLIP interactions: 6 interactions with chain I, 5 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: I:V.133, I:I.150, I:V.151, I:F.183, I:V.190, I:L.193, J:I.75, J:P.77, J:F.81, J:F.85, J:L.88, A:F.52 PL9.24: 16 residues within 4Å: Chain D: C.178, H.179 Chain J: P.72, L.73, E.74, I.75, W.79, R.89, T.137, I.145, T.148, L.149 Chain K: Q.273 Chain O: F.7, L.11 Ligands: CLA.20 11 PLIP interactions: 9 interactions with chain J, 2 interactions with chain O Hydrophobic interactions: J:L.73, J:E.74, J:I.75, J:W.79, J:T.137, J:I.145, J:L.149, O:F.7, O:L.11 Hydrogen bonds: J:I.75, J:R.89 PL9.28: 13 residues within 4Å: Chain I: L.45, F.78, W.80, L.81 Chain J: V.52 Chain K: R.285, G.288, L.289 Chain L: Y.83, M.84, P.87 Ligands: PL9.8, SQD.29 5 PLIP interactions: 2 interactions with chain I, 2 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: I:L.45, I:L.81, L:M.84, L:P.87, J:V.52

2 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 Chain C: K.306, F.310 Chain D: R.66, N.70, L.73, M.84 Ligands: UMQ.6, PL9.7 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:L.73 Hydrogen bonds: D:N.70, B:W.32 Salt bridges: D:R.66, C:K.306 SQD.29: 9 residues within 4Å: Chain J: W.32, P.41 Chain K: K.306, F.310 Chain L: R.66, N.70, L.73 Ligands: UMQ.21, PL9.28 5 PLIP interactions: 2 interactions with chain J, 2 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: J:P.41 Hydrogen bonds: J:W.32, L:N.70 Salt bridges: L:R.66, K:K.306

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

FES.14: 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.30: 10 residues within 4Å: Chain L: 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 L, Metal complexes: L:C.158, L:H.160, L:C.176, L:H.179

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

BCR.15: 6 residues within 4Å: Chain F: T.110 Chain G: I.16, G.20 Chain H: F.15, L.19 Chain R: L.39 4 PLIP interactions: 2 interactions with chain H, 1 interactions with chain R, 1 interactions with chain F Hydrophobic interactions: H:F.15, H:L.19, R:L.39, F:T.110 BCR.31: 9 residues within 4Å: Chain J: V.43 Chain N: T.110 Chain O: I.16, G.20 Chain P: F.15, S.18, L.19 Chain Q: L.39, I.42 6 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain J, 2 interactions with chain P, 1 interactions with chain N Hydrophobic interactions: Q:L.39, Q:I.42, J:V.43, P:F.15, P:L.19, N:T.110

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
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
R

R
Q

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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