SMTL ID : 3cxh.1

Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-1-mer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 11 residues within 4Å: Chain O: E.140, P.141, L.147, G.150, S.151, N.152, Y.153 Chain W: K.20, T.21, Q.24, Q.25 6 PLIP interactions: 4 interactions with chain O, 2 interactions with chain W Hydrogen bonds: O:G.150, O:G.150, O:N.152, W:Q.24, O:E.140, O:E.140, O:Y.153 Water bridges: W:Q.25, O:Y.153

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

UMQ.2: 16 residues within 4Å: Chain A: W.401, D.402, S.427, M.428, M.429, R.430 Chain E: Y.27, V.30, S.38 Chain H: Y.31 Chain I: N.13, A.14, V.15, F.16, V.17 Ligands: 6PH.12 13 PLIP interactions: 4 interactions with chain A, 5 interactions with chain I, 2 interactions with chain H, 2 interactions with chain E Hydrogen bonds: A:S.427, A:M.428, A:R.430, A:R.430, I:N.13, I:A.14, I:V.17, H:Y.31, H:Y.31, E:Y.27, E:Y.27 Hydrophobic interactions: I:V.17 Water bridges: I:V.15 UMQ.14: 17 residues within 4Å: Chain L: W.401, D.402, S.427, M.428, M.429, R.430 Chain P: Y.27, V.30, S.38 Chain T: N.13, A.14, V.15, F.16, V.17, I.20 Ligands: 6PH.13, 7PH.22 11 PLIP interactions: 5 interactions with chain T, 1 interactions with chain S, 4 interactions with chain L, 1 interactions with chain P Hydrophobic interactions: T:V.17, T:I.20 Hydrogen bonds: T:N.13, T:A.14, T:V.17, S:Y.31, L:S.427, L:M.428, L:R.430, L:R.430, P:Y.27

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

HEM.3: 22 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, V.65, R.79, H.82, A.83, A.86, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, Y.274 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:A.51, C:A.83, C:A.86, C:T.127, C:Y.184, C:P.187 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.82, C:H.183 pi-Cation interactions: C:H.183 Metal complexes: C:H.82, C:H.183 HEM.4: 24 residues within 4Å: Chain C: W.30, M.32, G.33, S.34, L.36, G.37, F.89, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.198, L.201, S.206, S.207 27 PLIP interactions: 27 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:F.89, C:L.113, C:L.113, C:W.114, C:W.114, C:V.118, C:I.120, C:F.121, C:V.194, C:V.194, C:L.198, C:L.201 Hydrogen bonds: C:G.33, C:S.105, C:S.207 Water bridges: C:W.30, C:M.32, C:S.34 Salt bridges: C:H.96, C:K.99, C:K.99, C:R.110 pi-Stacking: C:H.96 Metal complexes: C:H.96, C:H.197 HEM.9: 20 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, A.111, P.113, P.114, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:A.111, D:P.113, D:P.114, D:I.119, D:I.130, D:L.133, D:L.134, D:I.162, D:M.164, D:L.168 Hydrogen bonds: D:Y.129, D:Y.129, D:A.163 Water bridges: D:R.123 Salt bridges: D:R.123 pi-Stacking: D:H.44 pi-Cation interactions: D:H.44 Metal complexes: D:H.44 HEM.16: 21 residues within 4Å: Chain N: L.40, Q.43, I.44, G.47, I.48, M.50, V.65, R.79, H.82, A.83, A.86, F.89, T.127, A.128, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274 14 PLIP interactions: 14 interactions with chain N, Hydrophobic interactions: N:L.40, N:Q.43, N:I.48, N:A.83, N:A.86, N:F.89, N:T.127, N:Y.184, N:Y.184 Salt bridges: N:R.79, N:R.79 pi-Stacking: N:H.183 Metal complexes: N:H.82, N:H.183 HEM.17: 19 residues within 4Å: Chain N: W.30, G.33, L.36, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, V.194, H.197, L.198, L.201, S.206, S.207 23 PLIP interactions: 23 interactions with chain N, Hydrophobic interactions: N:L.36, N:L.36, N:L.113, N:L.113, N:I.120, N:L.198, N:L.201 Hydrogen bonds: N:W.30, N:G.33, N:S.105, N:S.207 Water bridges: N:M.32, N:S.34 Salt bridges: N:H.96, N:K.99, N:K.99, N:R.110 pi-Stacking: N:H.96, N:H.96, N:H.197, N:H.197 Metal complexes: N:H.96, N:H.197 HEM.21: 19 residues within 4Å: Chain O: V.39, C.40, C.43, H.44, N.108, A.111, P.113, P.114, I.119, R.123, Y.129, I.130, L.134, F.157, I.162, A.163, M.164, V.167, L.168 15 PLIP interactions: 15 interactions with chain O, Hydrophobic interactions: O:V.39, O:A.111, O:P.113, O:I.119, O:I.130, O:L.134, O:I.162, O:M.164, O:V.167, O:L.168 Hydrogen bonds: O:Y.129, O:A.163 Salt bridges: O:R.123 pi-Cation interactions: O:H.44 Metal complexes: O:H.44 HEM.24: 26 residues within 4Å: Chain W: R.22, C.23, C.26, H.27, V.37, G.38, P.39, L.41, I.44, S.49, G.50, Y.55, Y.57, T.58, N.61, W.68, M.73, Y.76, L.77, T.87, K.88, M.89, A.90, F.91, L.103, M.107 17 PLIP interactions: 17 interactions with chain W, Hydrophobic interactions: W:P.39, W:L.41, W:Y.55, W:Y.76, W:L.77, W:A.90, W:F.91 Hydrogen bonds: W:G.50, W:Q.51, W:Y.57, W:T.58, W:N.61, W:W.68, W:T.87, W:K.88 pi-Stacking: W:Y.76 Metal complexes: W:H.27

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.5: 21 residues within 4Å: Chain C: I.122, I.125, F.129, L.130, M.139, G.143, V.146, I.147, F.179, I.269, V.270, P.271, E.272, L.275, F.278, Y.279, M.295, F.296, I.299 Chain P: C.150, H.151 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.125, C:F.129, C:F.129, C:L.130, C:I.147, C:F.179, C:L.275, C:F.278 Hydrogen bonds: C:E.272 SMA.18: 19 residues within 4Å: Chain E: C.150, H.151 Chain N: I.122, I.125, F.129, M.139, G.143, V.146, I.147, F.179, I.269, P.271, E.272, L.275, F.278, Y.279, L.282, M.295, F.296 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:F.129, N:F.129, N:V.146, N:I.147, N:F.179, N:L.275, N:F.278, N:L.282 Hydrogen bonds: N:E.272

2 x 8PE: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate(Non-covalent)

8PE.6: 19 residues within 4Å: Chain C: W.29, F.94, M.95, A.98, Y.102, Y.103, P.209, F.278, T.317, F.326, F.327, V.330, F.333, Y.359 Chain G: E.81 Chain H: R.50, F.51, V.58 Ligands: CN6.7 11 PLIP interactions: 3 interactions with chain H, 8 interactions with chain C Hydrophobic interactions: H:F.51, C:W.29, C:W.29, C:F.278, C:F.326, C:V.330 Salt bridges: H:R.50, H:R.50 Hydrogen bonds: C:Y.102, C:Y.102, C:Y.103 8PE.19: 18 residues within 4Å: Chain N: W.29, F.94, M.95, A.98, Y.102, Y.103, F.278, T.317, K.323, F.326, F.327, V.330, F.331, F.333, V.334, Y.359 Chain R: E.81 Chain S: R.50 13 PLIP interactions: 10 interactions with chain N, 1 interactions with chain R, 2 interactions with chain S Hydrophobic interactions: N:W.29, N:F.94, N:F.278, N:F.326, N:V.330, N:F.331, N:F.333, N:V.334 Hydrogen bonds: N:Y.103, R:E.81 Salt bridges: N:K.323, S:R.50, S:R.50

2 x CN6: (2R,5R,11S,14R)-2-(butanoyloxy)-5,8,11-trihydroxy-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate(Non-covalent)

CN6.7: 17 residues within 4Å: Chain C: N.27, Y.28, W.29, M.32, F.88, M.95, V.231, L.235, I.239 Chain D: Y.220, I.224, K.227, K.228 Chain G: H.84 Chain H: R.50, F.51 Ligands: 8PE.6 16 PLIP interactions: 2 interactions with chain H, 8 interactions with chain D, 4 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: H:F.51, D:I.224, C:Y.28, C:F.88, C:I.239 Hydrogen bonds: H:R.50, D:Y.220, C:Y.28 Water bridges: D:K.227, D:K.227, G:H.84 Salt bridges: D:K.227, D:K.228, D:K.228, D:K.235, G:H.84 CN6.20: 14 residues within 4Å: Chain N: N.27, Y.28, W.29, M.32, F.88, M.91, V.231, L.235 Chain O: Y.220, I.224, K.227, K.228 Chain R: H.84 Chain S: R.50 13 PLIP interactions: 7 interactions with chain O, 1 interactions with chain R, 1 interactions with chain S, 4 interactions with chain N Hydrophobic interactions: O:I.224, N:F.88, N:F.88 Water bridges: O:K.227, O:K.235 Salt bridges: O:K.227, O:K.228, O:K.228, O:K.235, R:H.84, S:R.50 Hydrogen bonds: N:Y.28, N:Y.28

2 x 9PE: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate(Non-covalent)

9PE.8: 10 residues within 4Å: Chain C: T.112, N.115, I.119, A.192, I.195, M.196, M.199 Chain N: F.3, N.7, Y.9 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain N Hydrophobic interactions: C:I.119, C:A.192, C:I.195 Hydrogen bonds: C:T.112, C:N.115, N:N.7 Water bridges: C:S.108, C:P.109 9PE.15: 10 residues within 4Å: Chain C: F.3, N.7, Y.9, L.12 Chain N: T.112, N.115, V.116, I.195, M.196, M.199 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain C Hydrophobic interactions: N:V.116, N:I.195, C:L.12 Hydrogen bonds: N:N.115, C:N.7

2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.10: 16 residues within 4Å: Chain C: I.42, I.77, M.237, F.245 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: G.40, A.41, S.43, T.44, T.47, F.48 Ligands: 6PH.12 7 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: C:I.42, C:M.237, D:L.216, E:T.44, E:F.48 Salt bridges: D:K.211 Hydrogen bonds: E:S.43 7PH.22: 15 residues within 4Å: Chain N: I.42, M.237, F.245 Chain O: L.208, K.211, T.212, I.215, L.216 Chain P: G.40, A.41, S.43, T.44, T.47 Ligands: 6PH.13, UMQ.14 5 PLIP interactions: 2 interactions with chain O, 2 interactions with chain P, 1 interactions with chain N Hydrophobic interactions: O:L.216, P:A.41, N:I.42 Salt bridges: O:K.211 Hydrogen bonds: P:S.43

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

FES.11: 10 residues within 4Å: Chain E: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.129, E:H.131, E:C.148, E:H.151 FES.23: 9 residues within 4Å: Chain P: C.129, H.131, L.132, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.129, P:H.131, P:C.148, P:H.151

2 x 6PH: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate(Non-covalent)

6PH.12: 12 residues within 4Å: Chain A: S.424 Chain C: L.38, I.226, F.227, L.230, V.233 Chain E: V.30, M.33, G.34, S.37 Ligands: UMQ.2, 7PH.10 7 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:S.424 Hydrophobic interactions: C:I.226, C:F.227, C:L.230, C:V.233 Salt bridges: C:H.222, D:K.230 6PH.13: 11 residues within 4Å: Chain L: S.424 Chain N: G.37, I.226, F.227, L.230, V.233 Chain P: V.30, G.34, S.37 Ligands: UMQ.14, 7PH.22 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:F.227, N:L.230, N:V.233 Salt bridges: N:H.222, O:K.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Solmaz, S.R. et al., Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. J.Biol.Chem. (2008)

Release Date

2008-05-13

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AL
Cytochrome b-c1 complex subunit 2, mitochondrial: BM
Cytochrome b: CN
Cytochrome c1, heme protein, mitochondrial: DO
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EP
Cytochrome b-c1 complex subunit 6: FQ
Cytochrome b-c1 complex subunit 7: GR
Cytochrome b-c1 complex subunit 8: HS
Cytochrome b-c1 complex subunit 9: IT
HEAVY CHAIN (VH) OF FV-FRAGMENT: JU
LIGHT CHAIN (VL) OF FV-FRAGMENT: KV
Cytochrome c iso-2: W

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
L

B
B

M
M

C
C

N
N

D
D

O
O

E
E

P
P

F
F

Q
Q

G
G

R
R

H
H

S
S

I
I

T
T

J
J

U
U

K
K

V
V

W
W

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 6

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 9

HEAVY CHAIN (VH) OF FV-FRAGMENT

LIGHT CHAIN (VL) OF FV-FRAGMENT

Cytochrome c iso-2

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