SMTL ID : 8q1b.1

III2-IV1 respiratory supercomplex from S. pombe

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.66, H.70, E.146 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.66, A:H.66, A:H.70, A:E.146, A:E.146 ZN.15: 4 residues within 4Å: Chain K: H.66, H.70, E.146 Chain L: W.278 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.66, K:H.70, K:E.146, K:E.146 ZN.38: 7 residues within 4Å: Chain X: C.120, T.121, G.122, H.128, C.143, E.145, C.146 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.120, X:H.128, X:C.143, X:C.146

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 15 residues within 4Å: Chain A: Q.352, S.450, S.453, M.454, N.455, R.456 Chain C: K.2, M.17, I.18, N.222, L.226 Chain I: Y.18 Ligands: PCF.3, PEF.4, PCF.5 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:L.226 Hydrogen bonds: C:N.222, A:Q.352, A:S.450, A:S.450, A:N.455, A:N.455, A:R.456 Salt bridges: C:K.2, A:R.456 CDL.12: 20 residues within 4Å: Chain C: S.27, Y.28, F.29, Y.94, L.95, I.97, G.98, R.99, Y.102, Y.103, F.326, W.327, F.329, V.330 Chain G: N.80 Chain H: M.49, R.52, E.56, V.60 Ligands: CDL.13 15 PLIP interactions: 1 interactions with chain G, 10 interactions with chain C, 4 interactions with chain H Hydrogen bonds: G:N.80, C:Y.28, C:Y.103, H:E.56 Hydrophobic interactions: C:Y.94, C:L.95, C:I.97, C:Y.102, C:Y.102, C:W.327, C:F.329, C:V.330, H:V.60 Salt bridges: H:R.52, H:R.52 CDL.13: 21 residues within 4Å: Chain C: Y.28, F.29, F.32, I.231, I.235 Chain D: A.282, M.285, W.286, K.288, R.289, K.296 Chain E: M.72 Chain G: N.80 Chain H: M.38, F.41, F.42, S.45, N.48, M.49, R.52 Ligands: CDL.12 13 PLIP interactions: 5 interactions with chain D, 4 interactions with chain H, 4 interactions with chain C Hydrophobic interactions: D:M.285, D:W.286, H:F.41, H:F.42, C:Y.28, C:F.29, C:F.32, C:I.235 Salt bridges: D:K.288, D:R.289, D:K.296, H:R.52 Hydrogen bonds: H:N.48 CDL.16: 17 residues within 4Å: Chain K: Q.352, S.450, S.453, M.454, N.455, R.456 Chain M: L.4, L.10, M.17, I.18, N.222, L.226 Chain S: Y.18 Chain T: W.35 Ligands: PCF.17, PEF.21, PCF.28 13 PLIP interactions: 7 interactions with chain K, 2 interactions with chain T, 3 interactions with chain M, 1 interactions with chain S Hydrophobic interactions: K:R.456, T:W.35, T:W.35, M:L.4, M:L.10, M:L.226, S:Y.18 Hydrogen bonds: K:Q.352, K:S.450, K:S.450, K:N.455, K:R.456 Salt bridges: K:R.456 CDL.26: 16 residues within 4Å: Chain M: S.27, Y.28, F.29, Y.94, I.97, G.98, R.99, Y.102, F.326, V.330 Chain Q: N.80 Chain R: M.49, R.52, E.56, V.60 Ligands: CDL.27 14 PLIP interactions: 8 interactions with chain M, 4 interactions with chain R, 2 interactions with chain Q Hydrophobic interactions: M:F.29, M:I.97, M:Y.102, M:Y.102, M:F.326, M:V.330 Hydrogen bonds: M:Y.28, M:Y.103, R:R.52, R:R.52, Q:N.80, Q:N.80 Salt bridges: R:R.52, R:R.52 CDL.27: 14 residues within 4Å: Chain M: Y.28, F.29 Chain N: A.282, M.285, W.286, K.288, R.289 Chain R: F.41, S.45, T.46, N.48, M.49, R.52 Ligands: CDL.26 9 PLIP interactions: 3 interactions with chain R, 4 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: R:F.41, N:W.286, M:Y.28, M:F.29 Hydrogen bonds: R:N.48 Salt bridges: R:R.52, N:K.288, N:R.289, N:K.296

4 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Covalent)(Non-covalent)

PCF.3: 7 residues within 4Å: Chain A: H.348, R.456 Chain C: M.1, K.2, I.3 Chain J: W.35 Ligands: CDL.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:R.456 Salt bridges: A:R.456 Hydrogen bonds: C:I.3 PCF.5: 16 residues within 4Å: Chain A: W.427, S.453, N.455 Chain E: Y.70, G.77, T.80, A.84 Chain I: R.12, R.13, N.14, F.17, Y.18, I.21 Ligands: CDL.2, PEF.4, PEF.10 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain E Hydrophobic interactions: I:I.21, E:A.84 Hydrogen bonds: I:Y.18 PCF.17: 7 residues within 4Å: Chain K: H.348, R.456 Chain M: M.1, I.3, L.4 Chain T: W.35 Ligands: CDL.16 8 PLIP interactions: 3 interactions with chain K, 1 interactions with chain T, 4 interactions with chain M Hydrogen bonds: K:R.456, M:I.3 Salt bridges: K:H.348, K:R.456 Hydrophobic interactions: T:W.35, M:I.3, M:L.4, M:L.4 PCF.28: 15 residues within 4Å: Chain K: D.428, N.455 Chain M: M.17 Chain O: Y.70, G.77, A.84 Chain S: R.12, R.13, N.14, F.17, Y.18, I.21 Ligands: CDL.16, PEF.21, PEF.24 7 PLIP interactions: 2 interactions with chain O, 3 interactions with chain S, 2 interactions with chain K Hydrophobic interactions: O:A.84, S:F.17, S:Y.18, S:I.21 Hydrogen bonds: O:Y.70, K:N.455 Salt bridges: K:D.428

10 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.4: 13 residues within 4Å: Chain A: S.450 Chain C: N.222, P.223, L.226, L.230, I.233 Chain D: Y.287, K.291 Chain E: M.76, T.80 Ligands: CDL.2, PCF.5, U10.8 8 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E, 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:Y.287, E:T.80, C:L.230, C:I.233 Salt bridges: D:K.291 Hydrogen bonds: C:N.222, C:N.222, A:S.450 PEF.10: 21 residues within 4Å: Chain C: I.42, V.45, F.81, N.241, F.245 Chain D: M.269, Q.272, V.273, V.276, L.277 Chain E: G.83, A.84, A.86, T.87, V.88, D.90, F.91 Chain I: K.29, D.33 Chain J: Q.49 Ligands: PCF.5 17 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D, 4 interactions with chain C, 3 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: E:A.84, E:T.87, E:V.88, E:F.91, E:F.91, D:V.273, D:V.276, D:L.277, C:I.42, C:V.45, C:F.81, C:F.81 Hydrogen bonds: D:Q.272, I:D.33, J:Q.49 Salt bridges: I:K.29, I:K.29 PEF.14: 15 residues within 4Å: Chain C: N.73 Chain E: H.89, L.92, A.93, S.96 Chain J: F.46, A.47, V.50, P.51 Chain M: V.154, F.156, I.157, D.160, L.161, L.164 8 PLIP interactions: 4 interactions with chain M, 3 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: M:V.154, M:F.156, M:D.160, M:L.164, E:L.92, J:P.51 Salt bridges: E:H.89, E:H.89 PEF.21: 16 residues within 4Å: Chain K: N.446, R.449, S.450 Chain M: C.38, N.222, P.223, L.226, I.227, L.230 Chain N: K.291 Chain O: V.73, M.76, T.80 Ligands: CDL.16, U10.20, PCF.28 9 PLIP interactions: 5 interactions with chain M, 2 interactions with chain N, 2 interactions with chain K Hydrophobic interactions: M:L.226, M:I.227, M:L.230, M:L.230 Hydrogen bonds: M:N.222, K:R.449, K:S.450 Salt bridges: N:K.291, N:K.291 PEF.22: 11 residues within 4Å: Chain C: P.155, D.160, L.161 Chain M: Y.74 Chain O: H.89, L.92, S.96 Chain T: A.47, V.50, P.51 Ligands: U10.20 7 PLIP interactions: 2 interactions with chain O, 3 interactions with chain T, 1 interactions with chain M, 1 interactions with chain C Hydrogen bonds: O:S.96, M:N.73 Salt bridges: O:H.89 Hydrophobic interactions: T:A.47, T:V.50, T:V.50, C:D.160 PEF.24: 20 residues within 4Å: Chain M: I.42, V.45, L.77, L.237, N.241 Chain N: M.269, Q.272, V.273, V.276, L.277 Chain O: G.83, A.84, A.86, T.87, D.90, F.91 Chain S: K.29, D.33 Chain T: Q.49 Ligands: PCF.28 15 PLIP interactions: 6 interactions with chain O, 4 interactions with chain N, 3 interactions with chain M, 2 interactions with chain S Hydrophobic interactions: O:A.84, O:T.87, O:F.91, O:F.91, N:Q.272, N:V.273, N:V.276, N:L.277, M:I.42, M:V.45, M:L.237 Hydrogen bonds: O:D.90, O:D.90 Salt bridges: S:K.29, S:K.29 PEF.33: 16 residues within 4Å: Chain U: Y.101, P.102, R.103, F.107, I.162, L.166 Chain W: L.24, L.28, W.63, F.64, V.81, L.85, F.92, E.96, L.99 Ligands: PEF.37 12 PLIP interactions: 7 interactions with chain W, 5 interactions with chain U Hydrophobic interactions: W:L.24, W:L.28, W:W.63, W:F.64, W:F.92, W:F.92, W:L.99, U:F.107, U:F.107, U:I.162 Hydrogen bonds: U:R.103 Salt bridges: U:R.103 PEF.35: 12 residues within 4Å: Chain 2: F.10, K.11, I.14, F.18, T.21, M.22 Chain U: F.327, A.331 Chain V: T.71, V.77, I.80, I.84 12 PLIP interactions: 1 interactions with chain U, 8 interactions with chain 2, 3 interactions with chain V Hydrophobic interactions: U:F.327, 2:F.10, 2:F.10, 2:I.14, 2:F.18, 2:F.18, 2:F.18, 2:T.21, V:V.77, V:I.80, V:I.84 Salt bridges: 2:K.11 PEF.37: 18 residues within 4Å: Chain W: M.60, F.64, M.67, S.68, A.71, N.72, H.77, L.85, F.89, F.92, I.221, A.225, H.239, H.240, N.241, G.242, C.245 Ligands: PEF.33 12 PLIP interactions: 12 interactions with chain W Hydrophobic interactions: W:F.64, W:F.64, W:F.89, W:F.92, W:I.221, W:A.225 Hydrogen bonds: W:N.72, W:N.241, W:N.241, W:G.242 Salt bridges: W:H.77, W:H.239 PEF.39: 15 residues within 4Å: Chain 4: W.109, T.115, L.116, F.117, W.118, N.123 Chain U: L.222 Chain W: A.35, F.49, Y.189, W.190, T.195, Y.206, F.207, I.214 16 PLIP interactions: 6 interactions with chain 4, 10 interactions with chain W Hydrophobic interactions: 4:W.109, 4:L.116, W:A.35, W:F.49, W:F.49, W:Y.206, W:Y.206, W:F.207, W:F.207, W:I.214 Hydrogen bonds: 4:T.115, 4:T.115, 4:F.117, 4:N.123, W:W.190, W:Y.206

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

HEM.6: 17 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, I.48, L.50, R.79, H.82, A.86, G.131, Y.132, L.134, P.135, H.183, Y.184, P.187, Y.274 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.40, C:I.48, C:L.50, C:L.134, C:Y.184, C:Y.184 Salt bridges: C:R.79, C:R.79 Metal complexes: C:H.82, C:H.183 HEM.7: 18 residues within 4Å: Chain C: W.30, G.33, L.36, L.93, H.96, I.97, R.99, S.105, R.110, W.114, G.117, V.118, I.120, F.121, S.194, H.197, S.206, S.207 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.93, C:I.97, C:W.114, C:W.114, C:I.120, C:F.121 Hydrogen bonds: C:S.105, C:S.207 Salt bridges: C:H.96, C:R.99, C:R.110 pi-Cation interactions: C:H.96 Metal complexes: C:H.96, C:H.197 HEM.18: 19 residues within 4Å: Chain M: Q.43, I.44, G.47, I.48, L.50, Y.54, V.65, R.79, H.82, A.83, A.86, T.124, G.131, Y.132, L.134, P.135, H.183, Y.184, P.187 10 PLIP interactions: 10 interactions with chain M, Hydrophobic interactions: M:I.44, M:I.48, M:L.50, M:T.124, M:L.134, M:Y.184 Salt bridges: M:R.79, M:R.79 Metal complexes: M:H.82, M:H.183 HEM.19: 20 residues within 4Å: Chain M: W.30, G.33, L.36, L.93, H.96, I.97, R.99, S.105, R.110, T.113, W.114, G.117, I.120, F.121, S.194, H.197, L.198, L.201, S.206, S.207 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:L.36, M:L.93, M:I.97, M:T.113, M:W.114, M:I.120, M:F.121, M:L.198 Hydrogen bonds: M:F.32, M:G.33, M:S.105, M:S.207 Salt bridges: M:H.96, M:R.99, M:R.99, M:R.110 Metal complexes: M:H.96, M:H.197

2 x U10: UBIQUINONE-10(Non-covalent)

U10.8: 16 residues within 4Å: Chain C: Y.16, M.17, E.22, A.37, V.41, I.44, I.48, S.194, L.198, M.221 Chain E: L.92, W.95 Chain M: I.126, L.182, M.186 Ligands: PEF.4 10 PLIP interactions: 2 interactions with chain E, 2 interactions with chain M, 6 interactions with chain C Hydrophobic interactions: E:L.92, E:W.95, M:I.126, M:L.182, C:Y.16, C:A.37, C:V.41, C:I.44, C:I.48, C:L.198 U10.20: 16 residues within 4Å: Chain C: L.151, L.164 Chain M: Y.16, M.17, A.37, V.41, I.44, I.48, L.49, S.194, V.195, L.198, M.221 Chain O: W.95 Ligands: PEF.21, PEF.22 7 PLIP interactions: 2 interactions with chain C, 4 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: C:L.151, C:L.164, M:I.44, M:I.48, M:L.49, M:V.195, O:W.95

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

HEC.9: 14 residues within 4Å: Chain D: C.102, C.105, H.106, A.173, P.175, R.185, Y.191, L.196, F.218, I.223, A.224, M.225, P.228, V.251 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:A.173, D:P.175, D:L.196, D:I.223, D:P.228, D:V.251 Hydrogen bonds: D:Y.191, D:Y.191, D:A.224 Salt bridges: D:R.185 Metal complexes: D:H.106 HEC.23: 19 residues within 4Å: Chain N: V.101, C.102, C.105, H.106, N.170, A.173, P.175, P.176, R.185, Y.191, I.192, L.195, L.196, F.218, A.224, M.225, P.228, L.229, V.251 14 PLIP interactions: 14 interactions with chain N, Hydrophobic interactions: N:V.101, N:A.173, N:P.175, N:P.176, N:I.192, N:L.195, N:L.196, N:A.224, N:L.229, N:V.251 Hydrogen bonds: N:Y.191, N:A.224 Salt bridges: N:R.185 Metal complexes: N:H.106

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

FES.11: 8 residues within 4Å: Chain E: C.172, H.174, L.175, G.176, C.177, C.191, H.194, S.196 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.172, E:C.172, E:H.174, E:C.191, E:H.194 FES.25: 8 residues within 4Å: Chain O: C.172, H.174, L.175, C.177, C.191, C.193, H.194, S.196 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.172, O:H.174, O:C.191, O:H.194

2 x HEA: HEME-A(Non-covalent)

HEA.29: 26 residues within 4Å: Chain U: S.36, S.39, I.42, R.43, Y.61, I.65, H.68, M.72, I.73, F.76, I.77, G.132, W.133, Y.378, H.385, L.388, S.389, L.393, L.396, V.428, F.432, R.445, R.446, S.468, L.472, F.475 25 PLIP interactions: 25 interactions with chain U, Hydrophobic interactions: U:I.42, U:I.65, U:F.76, U:I.77, U:W.133, U:L.388, U:L.393, U:L.393, U:L.396, U:V.428, U:L.472, U:L.472, U:F.475 Hydrogen bonds: U:S.39, U:S.39, U:R.43, U:Y.61, U:W.133, U:Q.435, U:R.446 Salt bridges: U:R.445, U:R.446 pi-Stacking: U:F.432 Metal complexes: U:H.68, U:H.385 HEA.30: 26 residues within 4Å: Chain U: W.133, W.243, V.250, Y.251, H.296, T.315, I.318, A.319, T.322, G.323, G.359, L.360, G.362, L.365, S.366, D.371, H.375, V.380, H.383, F.384, V.387, L.388 Chain V: L.41, I.44, P.85, I.88 22 PLIP interactions: 18 interactions with chain U, 4 interactions with chain V, Hydrophobic interactions: U:W.243, U:V.250, U:V.250, U:V.250, U:T.322, U:L.360, U:L.365, U:V.380, U:F.384, U:V.387, U:L.388, V:L.41, V:I.44, V:I.44, V:I.88 Hydrogen bonds: U:W.133, U:Y.251, U:Y.251 Salt bridges: U:H.375 pi-Stacking: U:H.296 pi-Cation interactions: U:H.247 Metal complexes: U:H.383

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

CU.31: 3 residues within 4Å: Chain U: H.247, H.296, H.297 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:H.247, U:H.296, U:H.297

1 x CA: CALCIUM ION(Non-covalent)

CA.32: 5 residues within 4Å: Chain U: E.45, L.46, A.48, G.50, P.448 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:E.45, U:G.50

1 x MG: MAGNESIUM ION(Non-covalent)

MG.34: 3 residues within 4Å: Chain U: H.375, D.376 Chain V: E.219 3 PLIP interactions: 1 interactions with chain U, 2 interactions with chain V Metal complexes: U:H.375, V:E.219, V:E.219

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.36: 7 residues within 4Å: Chain V: H.182, C.217, E.219, L.220, C.221, H.225, M.228 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:H.182, V:E.219, V:C.221, V:C.221, V:H.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moe, A. et al., Structure and function of the S. pombe III-IV-cyt c supercomplex. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-11-15

Peptides

Probable mitochondrial-processing peptidase subunit beta: AK
Cytochrome b-c1 complex subunit 2, mitochondrial: BL
Cytochrome b: CM
Cytochrome c1, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 6: FP
Cytochrome b-c1 complex subunit 7: GQ
Cytochrome b-c1 complex subunit 8: HR
Cytochrome b-c1 complex subunit 9: IS
Cytochrome b-c1 complex subunit 10: JT
Cytochrome c oxidase subunit 1: U
Cytochrome c oxidase subunit 2: V
Cytochrome c oxidase subunit 3: W
Cytochrome c oxidase subunit 4, mitochondrial: X
Cytochrome c oxidase polypeptide 5, mitochondrial: Y
Cytochrome c oxidase subunit 6, mitochondrial: Z
Cytochrome c oxidase subunit 7: 0
Cytochrome c oxidase polypeptide VIII, mitochondrial: 1
Cytochrome c oxidase subunit 9, mitochondrial: 2
Cytochrome c oxidase subunit 12, mitochondrial: 3
Cytochrome c oxidase subunit 13, mitochondrial: 4
Respiratory supercomplex factor 2 homolog C1565.01: 5
Unknown polypeptide: 6

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
L

B
B

L
M

C
C

M
N

D
D

N
O

E
E

O
P

F
F

P
Q

G
G

Q
R

H
H

R
S

I
I

S
T

J
J

T
U

U
a

V
b

W
c

X
d

Y
e

Z
f

0
g

1
h

2
i

3
j

4
k

5
l

6
m

Membrane

We predict this structure to be a membrane protein.
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Probable mitochondrial-processing peptidase subunit beta

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

Cytochrome b-c1 complex subunit 10

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase polypeptide 5, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 7

Cytochrome c oxidase polypeptide VIII, mitochondrial

Cytochrome c oxidase subunit 9, mitochondrial

Cytochrome c oxidase subunit 12, mitochondrial

Cytochrome c oxidase subunit 13, mitochondrial

Respiratory supercomplex factor 2 homolog C1565.01

Unknown polypeptide

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