SMTL ID : 6hwh.1 (1 other biounit)

Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-4-2-2-2-2-2-2-2-mer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: C.333, H.335, L.336, C.338, C.352, C.354, H.355, S.357 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:H.335, A:H.335, A:H.355 FES.16: 9 residues within 4Å: Chain N: C.333, H.335, L.336, C.338, C.352, C.354, H.355, S.357, P.371 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:H.335, N:H.335, N:H.355

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 21 residues within 4Å: Chain F: I.251, I.252, V.255, A.256, G.259, M.262, W.263, R.267 Chain K: W.91, A.115, A.116, A.119, F.120, T.123, C.126, W.134, E.137 Chain M: R.487, K.490, F.502 Ligands: CDL.14 14 PLIP interactions: 7 interactions with chain F, 4 interactions with chain K, 3 interactions with chain M Hydrophobic interactions: F:I.251, F:I.252, F:V.255, F:A.256, F:W.263, K:A.116, K:F.120, K:T.123, K:T.123, M:F.502 Hydrogen bonds: F:R.267 Salt bridges: F:R.267, M:R.487, M:K.490 CDL.10: 30 residues within 4Å: Chain E: X.11 Chain J: F.118, P.119, R.120, L.121, L.180, L.184, T.228, F.232 Chain K: I.95, F.99, A.102, V.118, V.125, L.128, V.129 Chain L: M.24, V.25, G.28, T.29, W.32, E.36, L.149, G.153, V.156, L.160, R.164, V.180, V.181, Y.184 25 PLIP interactions: 9 interactions with chain K, 8 interactions with chain L, 8 interactions with chain J Hydrophobic interactions: K:I.95, K:F.99, K:F.99, K:A.102, K:V.118, K:V.125, K:V.125, K:L.128, K:V.129, L:W.32, L:W.32, L:L.149, L:V.156, L:Y.184, L:Y.184, J:L.121, J:L.180, J:L.184, J:T.228, J:F.232 Salt bridges: L:R.164, L:R.164, J:R.120 Hydrogen bonds: J:R.120, J:L.121 CDL.13: 25 residues within 4Å: Chain F: I.258, M.262, R.267 Chain M: H.37, W.38, S.39, V.122, A.125, F.129, T.130, R.366, P.367, R.368, T.374, S.378, I.381, A.382, F.389, V.425, A.426, W.429, A.430, L.433 Ligands: MQ9.3, CDL.14 13 PLIP interactions: 11 interactions with chain M, 2 interactions with chain F Hydrophobic interactions: M:V.122, M:F.129, M:T.130, M:A.382, M:F.389, M:V.425, M:V.425, F:I.258, F:I.258 Hydrogen bonds: M:R.368 Salt bridges: M:H.37, M:R.366, M:R.368 CDL.14: 22 residues within 4Å: Chain J: Y.29, V.32, W.127 Chain K: W.90, W.91, L.94, L.97, S.98, F.120 Chain M: R.366, R.368, W.429, L.433, S.436, P.483, L.484, P.485, K.486, R.487, K.490 Ligands: CDL.2, CDL.13 16 PLIP interactions: 2 interactions with chain J, 7 interactions with chain K, 7 interactions with chain M Hydrophobic interactions: J:V.32, K:W.90, K:W.90, K:W.91, K:L.94, K:L.97, K:L.97, K:F.120, M:W.429 Hydrogen bonds: J:Y.29, M:R.366, M:S.436, M:K.486 Salt bridges: M:R.368, M:K.486, M:R.487 CDL.17: 20 residues within 4Å: Chain S: I.251, V.255, A.256, G.259, M.262, W.263, R.267 Chain X: W.91, A.115, A.119, F.120, T.123, C.126, G.127, W.134, G.135, E.137 Chain Z: R.487, K.490 Ligands: CDL.26 15 PLIP interactions: 7 interactions with chain S, 2 interactions with chain Z, 1 interactions with chain N, 5 interactions with chain X Hydrophobic interactions: S:I.251, S:V.255, S:W.263, S:W.263, X:A.115, X:F.120, X:T.123, X:T.123 Salt bridges: S:R.267, S:R.267, S:R.267, Z:R.487, Z:K.490, N:K.139 Hydrogen bonds: X:P.136 CDL.23: 29 residues within 4Å: Chain R: X.11 Chain W: F.118, P.119, R.120, L.121, L.180, L.184 Chain X: I.95, F.99, V.121, I.122, V.125, L.128, V.129 Chain Y: V.25, T.29, W.32, E.36, L.149, I.152, G.153, A.157, L.160, L.161, R.164, A.177, V.180, V.181, Y.184 22 PLIP interactions: 7 interactions with chain X, 10 interactions with chain Y, 5 interactions with chain W Hydrophobic interactions: X:I.95, X:F.99, X:V.121, X:I.122, X:V.125, X:L.128, X:V.129, Y:W.32, Y:W.32, Y:L.149, Y:I.152, Y:A.157, Y:L.160, Y:Y.184, Y:Y.184, W:L.184 Salt bridges: Y:R.164, Y:R.164, W:R.120 Hydrogen bonds: W:R.120, W:R.120, W:L.121 CDL.26: 20 residues within 4Å: Chain W: L.28, Y.29, V.32, F.131 Chain X: W.90, I.93, L.94, S.98, F.120, T.123 Chain Z: R.366, R.368, W.429, L.433, S.436, L.484, K.486, R.487 Ligands: CDL.17, CDL.27 18 PLIP interactions: 5 interactions with chain W, 9 interactions with chain Z, 4 interactions with chain X Hydrophobic interactions: W:L.28, W:V.32, W:V.32, W:F.131, Z:W.429, Z:W.429, X:W.90, X:W.90, X:I.93, X:F.120 Hydrogen bonds: W:Y.29, Z:R.366, Z:S.436, Z:L.484, Z:L.484 Salt bridges: Z:R.368, Z:K.486, Z:R.487 CDL.27: 28 residues within 4Å: Chain S: I.258, M.262, R.267, A.268 Chain Z: H.37, W.38, S.39, V.122, A.125, F.129, T.130, R.366, P.367, R.368, T.374, S.378, I.381, A.382, F.389, L.418, V.422, V.425, A.426, W.429, A.430, L.433 Ligands: CDL.26, MQ9.29 16 PLIP interactions: 14 interactions with chain Z, 2 interactions with chain S Hydrophobic interactions: Z:V.122, Z:T.130, Z:A.382, Z:F.389, Z:V.422, Z:V.422, Z:V.425, Z:A.426, Z:W.429, Z:W.429, S:I.258 Hydrogen bonds: Z:R.368, S:A.268 Salt bridges: Z:H.37, Z:R.366, Z:R.368

4 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.3: 20 residues within 4Å: Chain F: M.247, W.250, I.258 Chain M: M.121, L.124, A.125, F.128, F.129, F.303, W.307, V.340, L.343, I.376, A.380, I.381, Y.384, L.385, T.388, F.389 Ligands: CDL.13 19 PLIP interactions: 4 interactions with chain F, 15 interactions with chain M Hydrophobic interactions: F:W.250, F:W.250, F:I.258, M:L.124, M:L.124, M:F.128, M:F.129, M:F.303, M:W.307, M:L.343, M:I.376, M:A.380, M:I.381, M:I.381, M:Y.384, M:L.385, M:L.385 pi-Stacking: F:W.250, M:F.389 MQ9.15: 19 residues within 4Å: Chain M: A.25, R.28, Q.29, E.44, L.220, G.224, A.225, L.227, A.228, L.229, V.230, W.231, F.232, F.257 Chain Z: Y.20, H.21, A.25 Ligands: HEM.11, MQ9.28 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain Z Hydrophobic interactions: M:A.25, M:L.220, M:A.225, M:L.227, M:L.229, M:V.230, M:W.231, M:W.231, M:F.232, M:F.232, M:F.232, M:F.232, M:F.257, Z:Y.20 MQ9.28: 19 residues within 4Å: Chain M: Y.20, H.21, A.25, R.28 Chain Z: A.25, R.28, Q.29, E.44, L.220, G.224, A.225, L.227, A.228, L.229, W.231, F.232, F.257 Ligands: MQ9.15, HEM.25 12 PLIP interactions: 10 interactions with chain Z, 2 interactions with chain M Hydrophobic interactions: Z:Q.29, Z:L.220, Z:A.225, Z:L.227, Z:A.228, Z:L.229, Z:W.231, Z:F.232, Z:F.232, Z:F.257, M:Y.20, M:A.25 MQ9.29: 21 residues within 4Å: Chain S: G.246, M.247, W.250, I.258 Chain Z: M.121, V.122, L.124, A.125, F.128, L.148, F.303, W.307, V.340, L.343, Y.347, A.380, I.381, Y.384, L.385, F.389 Ligands: CDL.27 25 PLIP interactions: 20 interactions with chain Z, 5 interactions with chain S Hydrophobic interactions: Z:M.121, Z:V.122, Z:L.124, Z:L.124, Z:F.128, Z:F.128, Z:L.148, Z:F.303, Z:W.307, Z:V.340, Z:V.340, Z:L.343, Z:Y.347, Z:I.381, Z:I.381, Z:Y.384, Z:Y.384, Z:L.385, Z:L.385, Z:F.389, S:W.250, S:W.250, S:W.250, S:I.258 pi-Stacking: S:W.250

6 x CU: COPPER (II) ION(Non-covalent)

CU.4: 6 residues within 4Å: Chain G: C.273, E.275, C.277, H.281, M.284 Ligands: CU.5 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.273, G:C.277, G:H.281 CU.5: 5 residues within 4Å: Chain G: H.232, C.273, C.277, M.284 Ligands: CU.4 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.232, G:C.273, G:C.277 CU.8: 4 residues within 4Å: Chain J: H.264, H.313, H.314 Ligands: HAS.6 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:H.264, J:H.313, J:H.314 CU.18: 6 residues within 4Å: Chain T: H.232, C.273, C.277, H.281, M.284 Ligands: CU.19 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:C.273, T:C.277, T:H.281 CU.19: 5 residues within 4Å: Chain T: H.232, C.273, C.277, M.284 Ligands: CU.18 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:H.232, T:C.273, T:C.277 CU.22: 3 residues within 4Å: Chain W: H.264, H.313, H.314 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:H.264, W:H.313, W:H.314

4 x HAS: HEME-AS(Non-covalent)

HAS.6: 37 residues within 4Å: Chain G: S.53, A.56, S.57, V.60, V.64, L.109 Chain J: W.151, W.260, V.267, Y.268, I.270, A.271, H.313, H.314, Y.316, T.330, I.333, A.334, T.337, G.338, F.341, F.369, L.370, G.373, G.376, V.377, L.379, A.380, D.385, T.389, V.394, H.397, F.398, V.401, L.402, R.459 Ligands: CU.8 31 PLIP interactions: 28 interactions with chain J, 3 interactions with chain G, Hydrophobic interactions: J:W.260, J:V.267, J:V.267, J:I.270, J:T.330, J:A.334, J:F.341, J:F.369, J:F.369, J:L.370, J:V.377, J:V.377, J:L.379, J:L.379, J:V.394, J:F.398, J:F.398, J:V.401, J:V.401, J:L.402, G:A.56, G:V.64, G:L.109 Hydrogen bonds: J:Y.268 Salt bridges: J:R.459 pi-Stacking: J:H.313, J:H.397, J:H.397 pi-Cation interactions: J:H.264, J:H.264 Metal complexes: J:H.397 HAS.7: 30 residues within 4Å: Chain J: I.50, F.52, F.53, G.56, L.57, A.59, L.60, L.62, R.63, Y.79, F.83, H.86, G.87, M.90, L.91, W.151, Y.392, V.395, F.398, H.399, L.402, F.403, F.446, H.449, R.459, R.460, S.481, L.484, G.485, M.488 23 PLIP interactions: 23 interactions with chain J, Hydrophobic interactions: J:I.50, J:F.52, J:F.52, J:F.53, J:L.60, J:L.62, J:F.83, J:M.90, J:L.91, J:Y.392, J:V.395, J:F.398, J:F.398 Hydrogen bonds: J:R.63, J:Y.79, J:F.83, J:W.151, J:R.460 Salt bridges: J:R.459, J:R.460 pi-Stacking: J:F.446 Metal complexes: J:H.86, J:H.399 HAS.20: 37 residues within 4Å: Chain T: A.56, S.57, V.60, V.64, P.102, I.105, L.109 Chain W: W.151, W.260, V.267, Y.268, I.270, A.271, H.313, H.314, T.330, I.333, A.334, T.337, G.338, F.341, F.369, G.373, G.376, V.377, I.378, L.379, A.380, D.385, T.389, V.394, H.397, F.398, V.401, L.402, T.405, R.459 29 PLIP interactions: 24 interactions with chain W, 5 interactions with chain T, Hydrophobic interactions: W:W.260, W:V.267, W:I.270, W:A.271, W:T.330, W:F.341, W:F.369, W:F.369, W:V.377, W:I.378, W:L.379, W:V.394, W:F.398, W:F.398, W:V.401, W:V.401, W:L.402, T:A.56, T:V.60, T:V.64, T:P.102, T:I.105 Hydrogen bonds: W:Y.268, W:D.385 Salt bridges: W:R.459 pi-Stacking: W:H.314, W:H.397 pi-Cation interactions: W:H.264 Metal complexes: W:H.397 HAS.21: 31 residues within 4Å: Chain W: I.50, F.52, F.53, G.56, L.57, A.59, L.60, L.62, R.63, Y.79, F.83, H.86, G.87, M.90, L.91, W.151, Y.392, V.395, F.398, H.399, L.402, F.403, T.445, F.446, R.459, R.460, Y.461, S.481, L.484, G.485, M.488 26 PLIP interactions: 26 interactions with chain W, Hydrophobic interactions: W:I.50, W:F.52, W:F.52, W:F.53, W:A.59, W:L.60, W:L.62, W:F.83, W:M.90, W:L.91, W:V.395, W:F.398, W:L.402, W:F.403, W:T.445 Hydrogen bonds: W:R.63, W:Y.79, W:F.83, W:W.151, W:R.460, W:Y.461 Salt bridges: W:R.459, W:R.460 pi-Stacking: W:F.446 Metal complexes: W:H.86, W:H.399

4 x HEC: HEME C(Non-covalent)(Covalent)

HEC.9: 9 residues within 4Å: Chain 0: T.93, F.158, G.178, D.183, L.184, N.202 Chain J: M.161, H.162 Ligands: HEC.30 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain 0, Hydrophobic interactions: J:M.161 Hydrogen bonds: 0:T.93, 0:N.202 HEC.30: 13 residues within 4Å: Chain 0: S.60, D.74, A.86, V.87, F.89, T.93, R.95, M.96, Q.201 Chain A: S.341, L.342, Y.343 Ligands: HEC.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain 0, Hydrophobic interactions: A:L.342 Hydrogen bonds: 0:Q.201 HEC.31: 11 residues within 4Å: Chain 1: S.60, A.86, V.87, F.89, S.92, T.93, G.94, R.95, M.96, Q.201 Ligands: HEC.32 1 PLIP interactions: 1 interactions with chain 1, Hydrogen bonds: 1:Q.201 HEC.32: 12 residues within 4Å: Chain 1: S.92, T.93, G.94, N.161, C.162, G.178, D.183, L.184, Q.201, N.202, M.203 Ligands: HEC.31 1 PLIP interactions: 1 interactions with chain 1, Hydrogen bonds: 1:N.202

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

HEM.11: 23 residues within 4Å: Chain M: F.40, G.43, E.44, A.46, L.47, I.120, H.123, L.124, R.126, I.127, A.132, N.140, W.141, G.144, S.145, L.148, I.223, H.226, L.227, V.230, H.235, T.236 Ligands: MQ9.15 23 PLIP interactions: 23 interactions with chain M, Hydrophobic interactions: M:L.47, M:L.47, M:I.120, M:I.120, M:L.124, M:I.127, M:I.127, M:I.127, M:W.141, M:L.148, M:I.223, M:L.227, M:V.230 Hydrogen bonds: M:G.43, M:E.44, M:T.236 Salt bridges: M:H.123, M:R.126, M:R.126, M:H.235, M:H.235 Metal complexes: M:H.123, M:H.226 HEM.12: 25 residues within 4Å: Chain M: F.50, L.53, L.54, G.57, L.60, T.61, A.92, I.95, R.106, H.109, H.110, A.113, F.116, A.151, E.154, G.155, G.158, Y.159, P.162, H.211, I.212, P.216, N.282, Y.304 Chain Z: L.213 15 PLIP interactions: 14 interactions with chain M, 1 interactions with chain Z, Hydrophobic interactions: M:F.50, M:L.53, M:L.54, M:L.60, M:F.116, M:E.154, M:P.216, Z:L.213 Hydrogen bonds: M:N.282 Salt bridges: M:R.106, M:R.106, M:H.110 pi-Stacking: M:H.109, M:H.211 Metal complexes: M:H.109 HEM.24: 22 residues within 4Å: Chain M: L.213 Chain Z: F.50, L.53, L.54, G.57, V.58, L.60, T.61, F.64, R.106, H.109, H.110, A.113, E.154, G.155, G.158, Y.159, P.162, H.211, I.212, P.216, N.282 20 PLIP interactions: 1 interactions with chain M, 19 interactions with chain Z, Hydrophobic interactions: M:L.213, Z:F.50, Z:L.53, Z:L.53, Z:L.54, Z:V.58, Z:L.60, Z:E.154, Z:Y.159, Z:I.212, Z:P.216 Hydrogen bonds: Z:N.282 Salt bridges: Z:R.106, Z:R.106 pi-Stacking: Z:H.109, Z:H.211, Z:H.211, Z:H.211 Metal complexes: Z:H.109, Z:H.211 HEM.25: 24 residues within 4Å: Chain Z: F.40, G.43, A.46, L.47, I.120, H.123, L.124, R.126, I.127, A.132, R.137, N.140, W.141, G.144, S.145, L.147, L.148, I.223, H.226, L.227, V.230, H.235, T.236 Ligands: MQ9.28 26 PLIP interactions: 26 interactions with chain Z, Hydrophobic interactions: Z:A.46, Z:L.47, Z:L.47, Z:I.120, Z:I.120, Z:L.124, Z:I.127, Z:I.127, Z:I.127, Z:A.132, Z:W.141, Z:L.147, Z:L.148, Z:I.223, Z:L.227, Z:V.230, Z:V.230 Hydrogen bonds: Z:G.43, Z:T.236 Salt bridges: Z:H.123, Z:R.126, Z:R.126, Z:R.137, Z:H.235, Z:H.235 Metal complexes: Z:H.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wiseman, B. et al., Structure of a functional obligate complex III2IV2respiratory supercomplex from Mycobacterium smegmatis. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-11-07

Peptides

Ubiquinol-cytochrome c reductase iron-sulfur subunit: AN
Co-purified unknown transmembrane helices built as polyALA: BO
Co-purified unknown transmembrane helices built as polyALA: CP
Co-purified unknown peptide built as polyALA: DQ
Co-purified unknown peptide built as polyALA: ER
Cytochrome bc1 complex cytochrome c subunit: FS01
Cytochrome c oxidase subunit 2: GT
MSMEG_4693: HU
Uncharacterized protein MSMEG_4692/MSMEI_4575: IV
Cytochrome c oxidase subunit 1: JW
Cytochrome c oxidase polypeptide 4: KX
Cytochrome c oxidase subunit 3: LY
Ubiquinol-cytochrome C reductase QcrB: MZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
B

B
G

O
C

C
H

P
D

D
I

Q
E

E
J

R
F

F
M

S
K

0
i

1
j

G
P

T
L

H
R

U
N

I
T

V
O

J
V

W
Q

K
X

X
S

L
Z

Y
W

M
b

Z
Y

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol-cytochrome c reductase iron-sulfur subunit

Co-purified unknown transmembrane helices built as polyALA

Co-purified unknown transmembrane helices built as polyALA

Co-purified unknown peptide built as polyALA

Co-purified unknown peptide built as polyALA

Cytochrome bc1 complex cytochrome c subunit

Cytochrome c oxidase subunit 2

MSMEG_4693

Uncharacterized protein MSMEG_4692/MSMEI_4575

Cytochrome c oxidase subunit 1

Cytochrome c oxidase polypeptide 4

Cytochrome c oxidase subunit 3

Ubiquinol-cytochrome C reductase QcrB

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