SMTL ID : 2zt9.1

Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192 Chain B: E.78 Chain I: F.189 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain I, Hydrophobic interactions: A:F.44, A:Q.47, A:Q.47, A:F.48, A:M.54, A:T.55, A:Y.58, A:Y.58, A:T.128, A:F.131, A:F.131, A:F.131, A:L.138, A:Y.184, A:P.192, I:F.189, I:F.189 Salt bridges: A:R.83, A:R.83, A:R.87 Metal complexes: A:H.86, A:H.187 HEM.2: 26 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, V.122, A.125, T.128, M.199, H.202, F.203, I.206, I.211, S.212 Ligands: HEM.3 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:T.40, A:V.101, A:V.104, A:V.104, A:T.117, A:W.118, A:W.118, A:W.118, A:V.122, A:A.125, A:F.203 Hydrogen bonds: A:G.37, A:G.38, A:S.212 Water bridges: A:Y.34 Salt bridges: A:H.100, A:R.103, A:R.103, A:R.114 Metal complexes: A:H.100, A:H.202 HEM.3: 19 residues within 4Å: Chain A: V.30, N.31, Y.34, C.35, G.38, L.41, V.42, F.203, I.206, R.207, G.210, I.211 Chain B: N.25, V.39, F.40, V.43, I.44 Chain H: R.26 Ligands: HEM.2 14 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.34, A:V.42, A:F.203, A:F.203, A:I.211, B:V.39, B:F.40, B:F.40, B:V.43, B:I.44 Hydrogen bonds: A:I.211 Salt bridges: A:R.207 pi-Stacking: B:F.40 Metal complexes: H2O.1 HEM.10: 22 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, V.75, N.154, G.156, R.157, G.158, Q.159, V.160, Y.161, P.162 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.1, C:Y.1, C:P.2, C:W.4, C:W.4, C:A.5, C:N.71, C:V.75, C:N.154, C:R.157, C:Y.161 Hydrogen bonds: C:Y.1, C:N.71, C:N.71, C:N.71 Salt bridges: C:R.157 pi-Stacking: C:W.4 Metal complexes: C:H.26 HEM.14: 26 residues within 4Å: Chain A: F.189 Chain I: F.44, Q.47, F.48, G.51, F.52, M.54, T.55, Y.58, R.83, H.86, R.87, A.90, M.93, T.128, F.131, G.132, G.135, Y.136, L.138, P.139, Y.184, H.187, T.188, P.192 Chain J: E.78 22 PLIP interactions: 2 interactions with chain A, 20 interactions with chain I, Hydrophobic interactions: A:F.189, A:F.189, I:F.44, I:Q.47, I:Q.47, I:F.48, I:M.54, I:T.55, I:Y.58, I:Y.58, I:T.128, I:F.131, I:F.131, I:F.131, I:L.138, I:Y.184, I:P.192 Salt bridges: I:R.83, I:R.83, I:R.87 Metal complexes: I:H.86, I:H.187 HEM.15: 26 residues within 4Å: Chain I: 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, V.122, A.125, T.128, M.199, H.202, F.203, I.206, I.211, S.212 Ligands: HEM.16 21 PLIP interactions: 21 interactions with chain I, Hydrophobic interactions: I:T.40, I:V.101, I:V.104, I:V.104, I:T.117, I:W.118, I:W.118, I:W.118, I:V.122, I:A.125, I:F.203 Hydrogen bonds: I:G.37, I:G.38, I:S.212 Water bridges: I:Y.34 Salt bridges: I:H.100, I:R.103, I:R.103, I:R.114 Metal complexes: I:H.100, I:H.202 HEM.16: 19 residues within 4Å: Chain I: V.30, N.31, Y.34, C.35, G.38, L.41, V.42, F.203, I.206, R.207, G.210, I.211 Chain J: N.25, V.39, F.40, V.43, I.44 Chain P: R.26 Ligands: HEM.15 14 PLIP interactions: 6 interactions with chain J, 7 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: J:V.39, J:F.40, J:F.40, J:V.43, J:I.44, I:Y.34, I:V.42, I:F.203, I:F.203, I:I.211 pi-Stacking: J:F.40 Hydrogen bonds: I:I.211 Salt bridges: I:R.207 Metal complexes: H2O.1 HEM.23: 22 residues within 4Å: Chain K: Y.1, P.2, W.4, A.5, C.22, C.25, H.26, Q.60, L.70, N.71, V.72, G.73, A.74, V.75, N.154, G.156, R.157, G.158, Q.159, V.160, Y.161, P.162 19 PLIP interactions: 19 interactions with chain K, Hydrophobic interactions: K:Y.1, K:Y.1, K:P.2, K:W.4, K:W.4, K:A.5, K:N.71, K:V.75, K:N.154, K:R.157, K:Y.161 Hydrogen bonds: K:Y.1, K:N.71, K:N.71, K:N.71, K:Y.161 Salt bridges: K:R.157 pi-Stacking: K:W.4 Metal complexes: K:H.26

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

UMQ.4: 15 residues within 4Å: Chain A: N.74, E.75, V.76, N.77, F.78, W.80, L.81 Chain B: F.48, V.52 Chain C: N.253, R.254, W.257, F.261 Chain D: G.33, A.34 13 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:R.254, C:W.257, C:F.261, C:F.261, A:F.78, A:L.81, B:F.48, B:V.52 Hydrogen bonds: C:D.251, A:E.75, A:N.77, A:F.78, A:W.80 UMQ.5: 7 residues within 4Å: Chain A: N.3, Y.5, I.14, I.17, A.18 Ligands: UMQ.6, SQD.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.14, A:I.17 Hydrogen bonds: A:N.3 UMQ.6: 9 residues within 4Å: Chain A: Q.15, A.18, E.19, V.21, T.22 Chain B: W.32 Chain C: N.288 Ligands: UMQ.5, SQD.9 7 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:N.288, C:N.288, A:Q.15, A:E.19 Hydrophobic interactions: B:W.32, B:W.32, A:V.21 UMQ.17: 15 residues within 4Å: Chain I: N.74, E.75, V.76, N.77, F.78, W.80, L.81 Chain J: F.48, V.52 Chain K: N.253, R.254, W.257, F.261 Chain L: G.33, A.34 12 PLIP interactions: 4 interactions with chain K, 2 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: K:R.254, K:W.257, K:F.261, K:F.261, J:F.48, J:V.52, I:F.78, I:L.81 Hydrogen bonds: I:E.75, I:N.77, I:F.78, I:W.80 UMQ.18: 7 residues within 4Å: Chain I: N.3, Y.5, I.14, I.17, A.18 Ligands: UMQ.19, SQD.22 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:I.14, I:I.17 Hydrogen bonds: I:N.3 UMQ.19: 9 residues within 4Å: Chain I: Q.15, A.18, E.19, V.21, T.22 Chain J: W.32 Chain K: N.288 Ligands: UMQ.18, SQD.22 9 PLIP interactions: 2 interactions with chain K, 2 interactions with chain J, 5 interactions with chain I Hydrogen bonds: K:N.288, K:N.288, I:Q.15, I:E.19, I:E.19, I:T.22 Hydrophobic interactions: J:W.32, J:W.32, I:V.21

2 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.7: 19 residues within 4Å: Chain A: I.98, F.102, Y.105, A.125, V.129 Chain B: Y.80, P.83, V.84, I.87, M.101, V.104, L.108, I.109, V.132, F.133, G.136, V.139, T.140 Ligands: OPC.8 15 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:I.98, A:F.102, A:Y.105, A:Y.105, A:V.129, B:V.84, B:I.87, B:V.104, B:V.104, B:I.109, B:V.132, B:F.133, B:V.139 Hydrogen bonds: B:V.84 Metal complexes: H2O.1 CLA.20: 19 residues within 4Å: Chain I: I.98, F.102, Y.105, A.125, V.129 Chain J: Y.80, P.83, V.84, I.87, M.101, V.104, L.108, I.109, V.132, F.133, G.136, V.139, T.140 Ligands: OPC.21 15 PLIP interactions: 5 interactions with chain I, 9 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: I:I.98, I:F.102, I:Y.105, I:Y.105, I:V.129, J:V.84, J:I.87, J:V.104, J:V.104, J:I.109, J:V.132, J:F.133, J:V.139 Hydrogen bonds: J:V.84 Metal complexes: H2O.1

4 x OPC: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE(Non-covalent)

OPC.8: 15 residues within 4Å: Chain B: I.87, S.103, V.104, L.108, V.111, I.114, E.115, N.118, R.125, R.126, P.127, V.128, A.129, V.132 Ligands: CLA.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.87, B:V.111, B:I.114, B:V.132 Hydrogen bonds: B:E.115, B:N.118, B:V.128, B:A.129 OPC.13: 21 residues within 4Å: Chain A: M.92, M.96 Chain B: S.47, C.50 Chain C: P.37, Q.38 Chain E: A.3, Y.7, I.8 Chain F: E.4, L.11, S.12 Chain G: L.5, I.9 Chain H: M.1, T.5, W.8, L.11, L.12, F.15 Ligands: BCR.12 17 PLIP interactions: 7 interactions with chain H, 1 interactions with chain C, 2 interactions with chain G, 3 interactions with chain F, 1 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: H:W.8, H:W.8, H:L.11, H:L.12, H:L.12, H:F.15, H:F.15, G:L.5, G:I.9, F:L.11, F:L.11, A:M.92, E:A.3, E:Y.7, E:Y.7 Hydrogen bonds: C:Q.38, F:E.4 OPC.21: 15 residues within 4Å: Chain J: I.87, S.103, V.104, L.108, V.111, I.114, E.115, N.118, R.125, R.126, P.127, V.128, A.129, V.132 Ligands: CLA.20 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:I.87, J:V.111, J:I.114, J:V.132 Hydrogen bonds: J:N.118, J:V.128, J:A.129 OPC.26: 21 residues within 4Å: Chain I: M.92, M.96 Chain J: S.47, C.50 Chain K: P.37, Q.38 Chain M: A.3, Y.7, I.8 Chain N: E.4, L.11, S.12 Chain O: L.5, I.9 Chain P: M.1, T.5, W.8, L.11, L.12, F.15 Ligands: BCR.25 16 PLIP interactions: 7 interactions with chain P, 2 interactions with chain O, 1 interactions with chain I, 2 interactions with chain N, 3 interactions with chain M, 1 interactions with chain K Hydrophobic interactions: P:W.8, P:W.8, P:L.11, P:L.12, P:L.12, P:F.15, P:F.15, O:L.5, O:I.9, I:M.92, N:L.11, N:L.11, M:A.3, M:Y.7, M:Y.7 Hydrogen bonds: K:Q.38

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

SQD.9: 11 residues within 4Å: Chain B: W.32, P.33, Y.38 Chain C: K.275, V.279 Chain D: R.16, N.20, F.24, T.28 Ligands: UMQ.5, UMQ.6 6 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:F.24 Hydrogen bonds: D:N.20, B:W.32, B:Y.38 Salt bridges: D:R.16, C:K.275 SQD.22: 11 residues within 4Å: Chain J: W.32, P.33, Y.38 Chain K: K.275, V.279 Chain L: R.16, N.20, F.24, T.28 Ligands: UMQ.18, UMQ.19 6 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L, 2 interactions with chain J Salt bridges: K:K.275, L:R.16 Hydrophobic interactions: L:F.24 Hydrogen bonds: L:N.20, J:W.32, J:Y.38

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

FES.11: 10 residues within 4Å: Chain D: C.108, H.110, L.111, C.113, C.126, C.128, H.129, G.130, S.131, P.143 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.108, D:H.110, D:C.126, D:H.129 FES.24: 10 residues within 4Å: Chain L: C.108, H.110, L.111, C.113, C.126, C.128, H.129, G.130, S.131, P.143 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.108, L:H.110, L:C.126, L:H.129

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

BCR.12: 18 residues within 4Å: Chain A: I.32, F.33, I.39, L.99 Chain B: V.43 Chain F: I.16, F.17, W.20 Chain G: L.13, V.16, T.17, A.19, G.20, Y.23 Chain H: F.15, S.18, I.19 Ligands: OPC.13 20 PLIP interactions: 3 interactions with chain H, 6 interactions with chain A, 5 interactions with chain F, 5 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: H:F.15, H:I.19, H:I.19, A:I.32, A:I.32, A:F.33, A:F.33, A:I.39, A:L.99, F:I.16, F:I.16, F:F.17, F:F.17, F:W.20, G:L.13, G:A.19, G:Y.23, G:Y.23, G:Y.23, B:V.43 BCR.25: 18 residues within 4Å: Chain I: I.32, F.33, I.39, L.99 Chain J: V.43 Chain N: I.16, F.17, W.20 Chain O: L.13, V.16, T.17, A.19, G.20, Y.23 Chain P: F.15, S.18, I.19 Ligands: OPC.26 20 PLIP interactions: 6 interactions with chain I, 5 interactions with chain O, 5 interactions with chain N, 3 interactions with chain P, 1 interactions with chain J Hydrophobic interactions: I:I.32, I:I.32, I:F.33, I:F.33, I:I.39, I:L.99, O:L.13, O:A.19, O:Y.23, O:Y.23, O:Y.23, N:I.16, N:I.16, N:F.17, N:F.17, N:W.20, P:F.15, P:I.19, P:I.19, J:V.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baniulis, D. et al., Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120. J.Biol.Chem. (2009)

Release Date

2009-02-10

Peptides

Cytochrome b6: AI
Cytochrome b6-f complex subunit 4: BJ
Apocytochrome f: CK
Cytochrome b6-f complex iron-sulfur subunit 1: 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
A

B
B

J
B

C
C

K
C

D
D

L
D

E
E

M
E

F
F

N
F

G
G

O
G

H
H

P
H

Membrane

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

Cytochrome b6-f complex subunit 4

Apocytochrome f

Cytochrome b6-f complex iron-sulfur subunit 1

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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