SMTL ID : 5xte.1

Cryo-EM structure of human respiratory complex III (cytochrome bc1 complex)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x CDL: CARDIOLIPIN(Non-covalent)(Covalent)

CDL.1: 9 residues within 4Å: Chain A: R.40, I.41, S.44 Chain F: H.68 Chain I: S.27, A.28, F.32 Ligands: CDL.6, PEE.9 6 PLIP interactions: 1 interactions with chain I, 1 interactions with chain F, 4 interactions with chain A Hydrogen bonds: I:A.28 Salt bridges: F:H.68, A:R.40, A:R.40, A:R.40 Hydrophobic interactions: A:I.41 CDL.3: 11 residues within 4Å: Chain C: T.56, V.59, S.63 Chain G: T.35, D.36, W.37, R.38 Chain T: Y.154, I.155, D.158, W.162 11 PLIP interactions: 6 interactions with chain T, 3 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: T:Y.154, T:I.155, T:I.155, T:W.162, T:W.162, C:T.56, C:V.59, G:W.37 Hydrogen bonds: T:D.158, C:S.63 Salt bridges: G:R.38 CDL.6: 20 residues within 4Å: Chain A: I.34, N.36, V.37, R.40 Chain F: K.67, H.68 Chain H: V.216, Y.220, K.223, R.224, K.231 Chain I: A.28, N.31, F.32, L.35, K.226, L.229, L.233, S.237 Ligands: CDL.1 24 PLIP interactions: 3 interactions with chain A, 9 interactions with chain I, 1 interactions with chain F, 11 interactions with chain H Hydrogen bonds: A:N.36, A:R.40, I:N.31, F:K.67, H:Y.220, H:Y.220, H:R.224 Salt bridges: A:R.40, I:K.226, I:K.226, H:K.223, H:R.224, H:R.224, H:K.231 Hydrophobic interactions: I:A.28, I:F.32, I:F.32, I:L.35, I:L.233, I:L.233, H:V.216, H:Y.220, H:Y.220, H:Y.220 CDL.10: 13 residues within 4Å: Chain I: L.12, A.190, T.193, L.194, L.196, L.197, H.200 Chain T: L.12, H.15, S.16, T.193, L.197, H.200 13 PLIP interactions: 4 interactions with chain T, 9 interactions with chain I Hydrophobic interactions: T:L.12, T:L.197, I:L.12, I:A.190, I:T.193, I:L.194, I:L.196, I:L.196, I:L.197, I:L.197 Salt bridges: T:H.15, T:H.200 Hydrogen bonds: I:H.200 CDL.11: 11 residues within 4Å: Chain I: I.155, D.158, L.159, W.162 Chain N: V.55, T.56, V.59, S.60 Chain R: T.35, W.37 Ligands: PEE.26 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain R, 1 interactions with chain N Hydrophobic interactions: I:I.155, I:L.159, I:W.162, R:W.37, N:V.55 CDL.13: 12 residues within 4Å: Chain I: R.4, M.10, F.17, I.18, H.220, T.224 Chain K: F.336, R.436, W.443, L.444, R.445 Ligands: PEE.14 10 PLIP interactions: 5 interactions with chain I, 5 interactions with chain K Hydrophobic interactions: I:F.17, I:F.17, I:I.18, K:R.445 Salt bridges: I:R.4, I:H.220, K:R.436, K:R.445 Hydrogen bonds: K:L.444, K:R.445 CDL.15: 11 residues within 4Å: Chain L: V.37, R.40, I.41, S.44 Chain Q: H.68 Chain T: S.27, A.28, W.29, F.32 Ligands: CDL.21, PEE.24 8 PLIP interactions: 5 interactions with chain L, 2 interactions with chain T, 1 interactions with chain Q Hydrophobic interactions: L:V.37, L:I.41, T:F.32 Salt bridges: L:R.40, L:R.40, L:R.40, Q:H.68 Hydrogen bonds: T:A.28 CDL.21: 19 residues within 4Å: Chain L: V.29, I.34, R.40 Chain Q: K.67, H.68 Chain S: V.216, P.217, Y.220, K.223, R.224, K.231 Chain T: A.28, F.32, L.35, K.226, L.229, G.230, L.233 Ligands: CDL.15 18 PLIP interactions: 5 interactions with chain T, 3 interactions with chain L, 9 interactions with chain S, 1 interactions with chain Q Hydrophobic interactions: T:L.35, T:L.229, L:V.29, L:I.34, S:V.216, S:P.217, S:Y.220 Hydrogen bonds: T:N.31, L:R.40, S:Y.220, Q:H.68 Salt bridges: T:K.226, T:K.226, S:K.223, S:K.223, S:R.224, S:R.224, S:K.231 CDL.25: 14 residues within 4Å: Chain R: W.23 Chain T: R.4, F.17, I.18, F.219, H.220, T.224 Chain V: F.336, R.436, W.443, L.444, R.445 Ligands: PLX.17, PEE.26 15 PLIP interactions: 6 interactions with chain T, 7 interactions with chain V, 2 interactions with chain R Hydrophobic interactions: T:F.17, T:I.18, T:F.219, T:T.224, V:L.444, V:L.444, R:W.23, R:W.23 Salt bridges: T:R.4, T:H.220, V:R.436, V:R.445, V:R.445 Hydrogen bonds: V:L.444, V:R.445

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

FES.2: 9 residues within 4Å: Chain C: C.139, H.141, L.142, G.143, C.144, C.158, H.161, S.163, P.175 2 PLIP interactions: 2 interactions with chain C, Metal complexes: C:H.141, C:H.161 FES.16: 9 residues within 4Å: Chain N: C.139, H.141, L.142, C.144, C.158, C.160, H.161, S.163, P.175 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:H.141, N:C.158, N:H.161

6 x PEE: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.4: 12 residues within 4Å: Chain C: A.50, N.53, A.54, F.58 Chain D: D.36 Chain H: H.200, M.204, K.207, M.208 Chain I: L.235, M.239 Ligands: PLX.12 7 PLIP interactions: 1 interactions with chain I, 3 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: I:L.235, C:A.54, C:F.58, C:F.58, H:M.208 Salt bridges: H:H.200, H:K.207 PEE.9: 21 residues within 4Å: Chain A: E.43, V.48 Chain I: W.29, I.91, F.94, L.95, I.97, G.98, R.99, L.101, Y.102, Y.103, W.271, F.275, I.297, M.315, Q.321, Y.324, W.325, L.331 Ligands: CDL.1 18 PLIP interactions: 17 interactions with chain I, 1 interactions with chain A Hydrophobic interactions: I:W.29, I:W.29, I:I.91, I:I.97, I:L.101, I:Y.102, I:Y.102, I:Y.103, I:W.271, I:F.275, I:I.297, I:W.325, I:W.325, I:W.325, I:L.331 Hydrogen bonds: I:Y.103, I:Q.321, A:E.43 PEE.14: 8 residues within 4Å: Chain I: I.41, H.220 Chain K: R.436, S.439, F.442, L.444 Ligands: PLX.12, CDL.13 7 PLIP interactions: 4 interactions with chain I, 3 interactions with chain K Hydrophobic interactions: I:I.41, I:I.41 Salt bridges: I:H.220, I:H.220 Hydrogen bonds: K:R.436, K:S.439, K:S.439 PEE.19: 14 residues within 4Å: Chain N: Y.49, A.50, N.53, A.54, V.55 Chain S: H.200, M.204, K.207, M.211, M.212 Chain T: L.81, L.235, M.239 Ligands: PLX.17 9 PLIP interactions: 1 interactions with chain T, 3 interactions with chain S, 5 interactions with chain N Hydrophobic interactions: T:L.81, N:A.50, N:A.54, N:V.55 Hydrogen bonds: S:H.200, S:K.207, N:Y.49, N:N.53 Salt bridges: S:K.207 PEE.24: 18 residues within 4Å: Chain L: S.44, V.48, F.52 Chain T: W.29, F.94, L.95, G.98, Y.102, Y.103, L.119, M.315, Q.321, Y.324, W.325, L.331, L.332, T.335 Ligands: CDL.15 13 PLIP interactions: 13 interactions with chain T Hydrophobic interactions: T:W.29, T:F.94, T:L.95, T:Y.102, T:L.119, T:Y.324, T:W.325, T:W.325, T:L.331, T:L.332 Hydrogen bonds: T:Y.102, T:Y.103, T:Q.321 PEE.26: 14 residues within 4Å: Chain N: T.44, A.48, A.51 Chain R: A.34 Chain T: L.9, M.10, I.13, H.220 Chain V: S.439, F.442, L.444 Ligands: CDL.11, PLX.17, CDL.25 10 PLIP interactions: 1 interactions with chain R, 2 interactions with chain V, 3 interactions with chain N, 4 interactions with chain T Hydrophobic interactions: R:A.34, N:T.44, N:A.48, N:A.51, T:L.9, T:I.13 Hydrogen bonds: V:S.439, V:F.442 Salt bridges: T:H.220, T:H.220

2 x HEC: HEME C(Non-covalent)

HEC.5: 22 residues within 4Å: Chain H: V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, I.116, R.120, Y.126, L.130, L.131, F.153, I.158, A.159, M.160, P.163, V.186 Chain N: H.161 16 PLIP interactions: 15 interactions with chain H, 1 interactions with chain N, Hydrophobic interactions: H:V.36, H:N.105, H:A.108, H:P.110, H:P.111, H:L.113, H:I.116, H:L.130, H:L.131, H:I.158, H:V.186 Hydrogen bonds: H:Y.126, H:A.159 Salt bridges: H:R.120, N:H.161 Metal complexes: H:H.41 HEC.20: 21 residues within 4Å: Chain C: H.161 Chain S: V.36, C.37, C.40, H.41, N.105, A.108, P.111, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, A.159, M.160, P.163, V.186, L.190 19 PLIP interactions: 18 interactions with chain S, 1 interactions with chain C, Hydrophobic interactions: S:V.36, S:A.108, S:I.116, S:V.127, S:V.127, S:L.130, S:L.131, S:L.131, S:I.158, S:I.158, S:P.163, S:V.186, S:L.190 Hydrogen bonds: S:Y.126, S:Y.126, S:A.159 Salt bridges: S:R.120, C:H.161 Metal complexes: S:H.41

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

HEM.7: 21 residues within 4Å: Chain I: L.40, Q.43, I.44, G.47, L.48, L.50, A.51, R.79, H.82, A.83, A.86, T.125, G.129, L.132, P.133, F.178, H.181, F.182, P.185, F.186, Y.272 15 PLIP interactions: 15 interactions with chain I, Hydrophobic interactions: I:L.40, I:Q.43, I:I.44, I:L.48, I:L.50, I:L.50, I:T.125, I:L.132, I:F.178, I:F.182, I:F.186 Salt bridges: I:R.79, I:R.79 pi-Stacking: I:H.82 Metal complexes: I:H.181 HEM.8: 18 residues within 4Å: Chain I: W.30, G.33, S.34, L.36, F.89, L.93, H.96, I.97, R.99, S.105, Y.108, W.112, G.115, L.118, H.195, L.199, S.204, N.205 17 PLIP interactions: 17 interactions with chain I, Hydrophobic interactions: I:L.36, I:L.36, I:F.89, I:W.112, I:W.112, I:L.118, I:L.199, I:L.199 Hydrogen bonds: I:W.30, I:G.33, I:S.34, I:N.205 Salt bridges: I:H.96, I:R.99, I:R.99 Metal complexes: I:H.96, I:H.195 HEM.22: 19 residues within 4Å: Chain T: L.40, Q.43, I.44, G.47, L.48, A.51, I.65, R.79, H.82, A.83, A.86, F.89, G.129, L.132, F.178, H.181, F.182, P.185, Y.272 15 PLIP interactions: 15 interactions with chain T, Hydrophobic interactions: T:L.40, T:Q.43, T:Q.43, T:I.44, T:A.51, T:A.86, T:F.89, T:F.89, T:L.132, T:L.132, T:F.178, T:F.182 Salt bridges: T:R.79, T:R.79 Metal complexes: T:H.181 HEM.23: 19 residues within 4Å: Chain T: W.30, G.33, S.34, L.36, G.37, F.89, L.93, H.96, I.97, R.99, S.105, Y.108, G.115, L.118, H.195, L.196, L.199, S.204, N.205 16 PLIP interactions: 16 interactions with chain T, Hydrophobic interactions: T:L.36, T:L.36, T:F.89, T:L.93, T:L.118, T:L.196, T:L.199, T:L.199 Hydrogen bonds: T:S.34, T:S.105, T:N.205 Salt bridges: T:H.96, T:R.99, T:R.99 pi-Cation interactions: T:R.99 Metal complexes: T:H.96

3 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.12: 16 residues within 4Å: Chain C: Y.37, T.40, T.43, V.47 Chain D: F.14, T.17, F.20, A.21 Chain H: I.222 Chain I: I.225, A.228, L.235 Chain K: D.417, F.442 Ligands: PEE.4, PEE.14 10 PLIP interactions: 1 interactions with chain D, 3 interactions with chain I, 4 interactions with chain C, 1 interactions with chain H, 1 interactions with chain K pi-Cation interactions: D:F.20, C:Y.37 Hydrophobic interactions: I:I.225, I:A.228, I:L.235, C:T.43, C:V.47, H:I.222 Hydrogen bonds: C:T.44 Salt bridges: K:D.417 PLX.17: 16 residues within 4Å: Chain N: Y.37, T.40, T.43, T.44, V.47 Chain O: F.14, R.15, T.17, F.20, A.21 Chain T: L.231 Chain V: F.442, L.444 Ligands: PEE.19, CDL.25, PEE.26 8 PLIP interactions: 1 interactions with chain V, 4 interactions with chain N, 2 interactions with chain O, 1 interactions with chain T Salt bridges: V:D.417 Hydrophobic interactions: N:T.40, N:T.43, N:V.47, O:A.21, T:L.231 pi-Cation interactions: N:Y.37 Hydrogen bonds: O:T.17 PLX.18: 7 residues within 4Å: Chain R: R.8, L.12, W.16 Chain V: R.344, S.348, W.443, R.445 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain V Hydrophobic interactions: R:W.16 Hydrogen bonds: V:S.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, R. et al., Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Cell (2017)

Release Date

2017-08-30

Peptides

Cytochrome b-c1 complex subunit 8: AL
Cytochrome b-c1 complex subunit Rieske, mitochondrial: BM
Cytochrome b-c1 complex subunit Rieske, mitochondrial: CN
Cytochrome b-c1 complex subunit 9: DO
Cytochrome b-c1 complex subunit 6, mitochondrial: EP
Cytochrome b-c1 complex subunit 7: FQ
Cytochrome b-c1 complex subunit 10: GR
Cytochrome c1, heme protein, mitochondrial: HS
Cytochrome b: IT
Cytochrome b-c1 complex subunit 2, mitochondrial: JU
Cytochrome b-c1 complex subunit 1, mitochondrial: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
N

B
B

M
O

C
C

N
P

D
D

O
Q

E
E

P
R

F
F

Q
S

G
G

R
T

H
H

S
U

I
J

T
V

J
K

U
W

K
L

V
Y

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 10

Cytochrome c1, heme protein, mitochondrial

Cytochrome b

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b-c1 complex subunit 1, mitochondrial

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