SMTL ID : 8ab6.1

Complex III2 from Yarrowia lipolytica, combined datasets, consensus refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.00 Å

Oligo State

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

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: Q.43, L.44, G.47, I.48, L.50, A.51, V.65, R.79, H.82, A.83, A.86, F.89, L.124, T.127, A.128, G.131, Y.132, L.134, V.135, F.180, H.183, Y.184, P.187, Y.274 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Q.43, A:L.44, A:L.50, A:A.51, A:V.65, A:A.83, A:F.89, A:T.127, A:L.134, A:L.134, A:F.180, A:Y.184, A:Y.184 Water bridges: A:R.79 Salt bridges: A:R.79, A:R.79 Metal complexes: A:H.82, A:H.183 HEM.2: 22 residues within 4Å: Chain A: W.30, G.33, L.36, A.37, F.89, I.93, H.96, M.97, R.99, N.100, S.105, W.114, G.117, V.118, I.120, F.121, L.190, H.197, L.198, L.201, S.206, S.207 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:L.36, A:L.36, A:F.89, A:I.93, A:W.114, A:W.114, A:I.120, A:F.121, A:L.190, A:L.198, A:L.201, A:L.201 Hydrogen bonds: A:W.30, A:G.33, A:S.206, A:S.207 Water bridges: A:F.32, A:S.34 Salt bridges: A:H.96, A:R.99, A:R.99, A:R.110 Metal complexes: A:H.96, A:H.197 HEM.17: 24 residues within 4Å: Chain K: Q.43, L.44, G.47, I.48, L.50, A.51, V.65, R.79, H.82, A.83, A.86, F.89, L.124, T.127, A.128, G.131, Y.132, L.134, V.135, F.180, H.183, Y.184, P.187, Y.274 18 PLIP interactions: 18 interactions with chain K, Hydrophobic interactions: K:Q.43, K:L.44, K:L.50, K:A.51, K:V.65, K:A.83, K:F.89, K:T.127, K:L.134, K:L.134, K:F.180, K:Y.184, K:Y.184 Water bridges: K:R.79 Salt bridges: K:R.79, K:R.79 Metal complexes: K:H.82, K:H.183 HEM.18: 21 residues within 4Å: Chain K: W.30, G.33, L.36, A.37, F.89, I.93, H.96, M.97, R.99, N.100, S.105, W.114, G.117, V.118, I.120, F.121, H.197, L.198, L.201, S.206, S.207 23 PLIP interactions: 23 interactions with chain K, Hydrophobic interactions: K:L.36, K:L.36, K:F.89, K:I.93, K:W.114, K:W.114, K:I.120, K:F.121, K:L.198, K:L.201, K:L.201 Hydrogen bonds: K:W.30, K:G.33, K:S.206, K:S.207 Water bridges: K:F.32, K:S.34 Salt bridges: K:H.96, K:R.99, K:R.99, K:R.110 Metal complexes: K:H.96, K:H.197

4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.3: 14 residues within 4Å: Chain A: F.29, Y.94, Y.102, Y.103, A.317, K.323, G.327, I.330, C.331 Chain C: L.86 Chain H: Q.53, F.56, V.57 Ligands: CDL.13 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:F.29, A:Y.102, A:Y.102, A:I.330, A:I.330, H:F.56 Hydrogen bonds: A:Y.103 Water bridges: A:N.27, A:P.209, H:Q.53 PC1.15: 16 residues within 4Å: Chain E: D.445, S.470, M.472 Chain I: Y.8, V.12, K.13, N.15, F.18, V.19, I.22 Chain L: Y.66, I.69, G.73, S.76 Ligands: PTY.4, CDL.9 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain E, 1 interactions with chain L, 1 interactions with chain G Hydrophobic interactions: I:I.22 Hydrogen bonds: I:N.15 Salt bridges: E:D.445 Water bridges: L:Y.66, G:K.314 PC1.19: 13 residues within 4Å: Chain K: F.29, Y.94, Y.102, Y.103, A.317, G.327, I.330, C.331 Chain M: L.86 Chain R: Q.53, F.56, V.57 Ligands: CDL.28 9 PLIP interactions: 7 interactions with chain K, 2 interactions with chain R Hydrophobic interactions: K:F.29, K:Y.102, K:Y.102, K:I.330, R:F.56 Hydrogen bonds: K:Y.103 Water bridges: K:N.27, K:P.209, R:Q.53 PC1.30: 18 residues within 4Å: Chain B: Y.66, I.69, G.73, S.76, A.77 Chain O: D.445, S.470, M.472 Chain S: Y.8, V.12, K.13, N.15, F.18, V.19, I.22, L.23 Ligands: PTY.20, CDL.24 6 PLIP interactions: 1 interactions with chain O, 4 interactions with chain S, 1 interactions with chain Q Salt bridges: O:D.445 Hydrophobic interactions: S:V.19, S:I.22, S:L.23 Hydrogen bonds: S:N.15 Water bridges: Q:K.314

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.4: 17 residues within 4Å: Chain A: S.34, A.37, L.38, H.222, S.226, F.227, D.229, L.230, V.233, F.234 Chain E: N.467 Chain G: K.314 Chain L: I.69, F.72, S.76 Ligands: CDL.9, PC1.15 17 PLIP interactions: 8 interactions with chain A, 3 interactions with chain E, 3 interactions with chain L, 3 interactions with chain G Hydrophobic interactions: A:A.37, A:F.227, A:D.229, A:L.230, A:V.233, A:F.234, L:F.72, L:F.72, L:F.72 Salt bridges: A:H.222, A:H.222, G:K.314, G:K.314 Water bridges: E:N.467, E:N.467, E:S.470, G:K.314 PTY.8: 19 residues within 4Å: Chain B: G.79, A.80, K.81, A.82, T.83, V.84, Q.85, D.86 Chain K: F.77, L.237, F.240, F.245 Chain Q: L.292, K.295, A.296, V.299, I.300 Chain S: D.30 Ligands: LMT.7 9 PLIP interactions: 2 interactions with chain B, 4 interactions with chain K, 2 interactions with chain Q, 1 interactions with chain S Hydrophobic interactions: B:V.84, K:L.237, K:L.237, K:F.240, K:F.240 Water bridges: B:Q.85, Q:K.295 Salt bridges: Q:K.295 Hydrogen bonds: S:D.30 PTY.20: 18 residues within 4Å: Chain B: I.69, F.72, S.76 Chain K: S.34, A.37, L.38, H.222, P.223, S.226, F.227, D.229, L.230, F.234 Chain O: N.467, M.472 Chain Q: K.314 Ligands: CDL.24, PC1.30 16 PLIP interactions: 3 interactions with chain O, 2 interactions with chain B, 8 interactions with chain K, 3 interactions with chain Q Hydrogen bonds: O:N.467 Water bridges: O:N.467, O:S.470, Q:K.314 Hydrophobic interactions: B:F.72, B:F.72, K:A.37, K:L.38, K:F.227, K:D.229, K:L.230, K:F.234 Salt bridges: K:H.222, K:H.222, Q:K.314, Q:K.314 PTY.23: 19 residues within 4Å: Chain A: F.77, L.237, F.240, F.245 Chain G: L.292, K.295, A.296, V.299, I.300 Chain I: D.30 Chain L: G.79, A.80, K.81, A.82, T.83, V.84, Q.85, D.86 Ligands: LMT.16 12 PLIP interactions: 1 interactions with chain I, 4 interactions with chain A, 3 interactions with chain L, 4 interactions with chain G Hydrogen bonds: I:D.30, L:K.81, L:D.86 Hydrophobic interactions: A:L.237, A:L.237, A:F.240, A:F.240, L:V.84, G:I.300 Water bridges: G:K.295, G:K.295 Salt bridges: G:K.295

10 x CDL: CARDIOLIPIN(Non-covalent)

CDL.5: 12 residues within 4Å: Chain A: T.108, P.109, R.110, V.111, L.112, S.115, L.303, I.307 Chain K: L.3, K.6, N.7, L.10 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain K Hydrophobic interactions: A:V.111, A:I.307 Hydrogen bonds: A:T.108, A:P.109, A:V.111, A:L.112, K:N.7 Water bridges: K:K.6, K:S.8 CDL.9: 12 residues within 4Å: Chain A: R.4, H.222 Chain E: H.364, M.471, M.472, R.473 Chain I: V.19 Chain J: W.38 Ligands: PTY.4, CDL.10, XP4.11, PC1.15 13 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J, 9 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: I:V.19, J:W.38 Hydrogen bonds: E:H.364, E:M.472, E:R.473, E:R.473 Water bridges: E:K.368, E:R.473 Salt bridges: E:H.364, E:K.368, E:R.473, A:R.4, A:H.222 CDL.10: 9 residues within 4Å: Chain A: A.2, L.3, R.4 Chain E: H.364, F.365, R.372, R.473 Ligands: CDL.9, XP4.11 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain E Hydrophobic interactions: A:R.4 Hydrogen bonds: A:L.3, E:R.473 Water bridges: E:R.372, E:R.473, E:R.473 Salt bridges: E:H.364, E:R.372, E:R.473, E:R.473 CDL.13: 17 residues within 4Å: Chain A: N.27, Y.28, F.29, F.32, L.35, T.232, F.236, M.239 Chain C: H.84 Chain H: T.46, R.49, T.50, Q.53, A.54, V.57 Ligands: PC1.3, CDL.14 19 PLIP interactions: 9 interactions with chain H, 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: H:Q.53, H:V.57, A:Y.28, A:F.29, A:F.32, A:T.232, A:F.236 Hydrogen bonds: H:R.49, H:Q.53, A:N.27, A:Y.28 Water bridges: H:R.49, H:R.49, C:H.84, C:H.84 Salt bridges: H:R.49, H:R.49, H:R.49, C:H.84 CDL.14: 12 residues within 4Å: Chain A: Y.28 Chain C: H.84 Chain G: V.308, K.311, K.312 Chain H: V.38, A.41, A.42, N.45, T.46, R.49 Ligands: CDL.13 14 PLIP interactions: 6 interactions with chain G, 6 interactions with chain H, 2 interactions with chain A Water bridges: G:K.311, G:K.319, A:K.228 Salt bridges: G:K.311, G:K.312, G:K.312, G:K.319, H:R.49 Hydrophobic interactions: H:V.38, A:Y.28 Hydrogen bonds: H:N.45, H:T.46, H:R.49, H:R.49 CDL.21: 12 residues within 4Å: Chain A: L.3, K.6, N.7, L.10 Chain K: T.108, P.109, R.110, V.111, L.112, S.115, L.303, I.307 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain K Hydrogen bonds: A:N.7, K:T.108, K:P.109, K:V.111, K:L.112 Water bridges: A:K.6, A:S.8 Hydrophobic interactions: K:V.111, K:I.307 CDL.24: 14 residues within 4Å: Chain K: R.4, H.222, S.226 Chain O: H.364, K.368, M.471, M.472, R.473 Chain S: N.15 Chain T: W.38 Ligands: PTY.20, CDL.25, XP4.26, PC1.30 13 PLIP interactions: 10 interactions with chain O, 2 interactions with chain K, 1 interactions with chain T Hydrogen bonds: O:H.364, O:M.472, O:R.473, O:R.473 Water bridges: O:K.368, O:R.464, O:R.473 Salt bridges: O:H.364, O:K.368, O:R.473, K:R.4, K:H.222 Hydrophobic interactions: T:W.38 CDL.25: 9 residues within 4Å: Chain K: A.2, L.3, R.4 Chain O: H.364, F.365, R.372, R.473 Ligands: CDL.24, XP4.26 10 PLIP interactions: 8 interactions with chain O, 2 interactions with chain K Hydrogen bonds: O:R.473, K:L.3 Water bridges: O:R.372, O:R.473, O:R.473 Salt bridges: O:H.364, O:R.372, O:R.473, O:R.473 Hydrophobic interactions: K:R.4 CDL.28: 16 residues within 4Å: Chain K: N.27, Y.28, F.29, F.32, L.35, T.232, F.236, M.239 Chain M: H.84 Chain R: T.46, R.49, T.50, Q.53, A.54 Ligands: PC1.19, CDL.29 17 PLIP interactions: 7 interactions with chain K, 3 interactions with chain M, 7 interactions with chain R Hydrophobic interactions: K:Y.28, K:F.29, K:F.32, K:T.232, K:F.236 Hydrogen bonds: K:N.27, K:Y.28, R:R.49, R:Q.53 Water bridges: M:H.84, M:H.84, R:R.49, R:R.49 Salt bridges: M:H.84, R:R.49, R:R.49, R:R.49 CDL.29: 12 residues within 4Å: Chain K: Y.28 Chain M: H.84 Chain Q: V.308, K.311, K.312 Chain R: V.38, A.41, A.42, N.45, T.46, R.49 Ligands: CDL.28 14 PLIP interactions: 6 interactions with chain R, 2 interactions with chain K, 6 interactions with chain Q Hydrophobic interactions: R:V.38, K:Y.28 Hydrogen bonds: R:N.45, R:T.46, R:R.49, R:R.49 Salt bridges: R:R.49, Q:K.311, Q:K.312, Q:K.312, Q:K.319 Water bridges: K:K.228, Q:K.311, Q:K.319

4 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.6: 12 residues within 4Å: Chain A: N.11, M.12, A.13, N.14, S.15, Y.16, V.17, L.195, I.199, H.202 Chain H: W.10 Chain K: M.12 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:M.12, A:Y.16, A:Y.16, A:Y.16, A:V.17, A:L.195, A:I.199 Hydrogen bonds: A:N.11, A:N.11, A:N.14, A:S.15, A:Y.16 Water bridges: A:D.19, A:H.202 LMT.7: 10 residues within 4Å: Chain B: V.84, Q.85, D.86, S.89 Chain K: F.74 Chain Q: E.288, L.292 Chain T: G.52, R.57 Ligands: PTY.8 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain T Hydrophobic interactions: B:V.84, B:Q.85 Hydrogen bonds: B:Q.85, B:D.86, B:D.86, B:S.89, T:G.52, T:R.57, T:R.57 LMT.16: 12 residues within 4Å: Chain A: F.74 Chain G: E.288, L.292 Chain J: L.49, I.50, G.52, V.53, R.57 Chain L: Q.85, D.86, S.89 Ligands: PTY.23 11 PLIP interactions: 7 interactions with chain J, 4 interactions with chain L Hydrophobic interactions: J:L.49, J:L.49, J:I.50, J:V.53, L:Q.85 Hydrogen bonds: J:G.52, J:R.57, J:R.57, L:Q.85, L:D.86, L:S.89 LMT.22: 10 residues within 4Å: Chain A: M.12 Chain K: N.11, M.12, N.14, S.15, Y.16, V.17, L.195, H.202 Chain R: W.10 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:M.12, K:Y.16, K:V.17, K:L.195 Hydrogen bonds: K:N.11, K:N.11, K:N.14, K:S.15, K:Y.16 Water bridges: K:D.19, K:H.202

2 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

XP4.11: 11 residues within 4Å: Chain E: R.372, S.376, R.473 Chain J: F.23, T.27, V.28, W.31, F.35, W.38 Ligands: CDL.9, CDL.10 12 PLIP interactions: 7 interactions with chain J, 5 interactions with chain E Hydrophobic interactions: J:F.23, J:W.31, J:F.35, J:F.35, J:W.38, J:W.38, J:W.38, E:R.473 Hydrogen bonds: E:S.376 Water bridges: E:R.372, E:R.473 Salt bridges: E:R.372 XP4.26: 11 residues within 4Å: Chain O: R.372, S.376, R.473 Chain T: F.23, T.27, V.28, W.31, F.35, W.38 Ligands: CDL.24, CDL.25 11 PLIP interactions: 5 interactions with chain O, 6 interactions with chain T Hydrophobic interactions: O:R.473, T:W.31, T:F.35, T:F.35, T:W.38, T:W.38, T:W.38 Hydrogen bonds: O:S.376 Water bridges: O:R.372, O:R.473 Salt bridges: O:R.372

2 x HEC: HEME C(Non-covalent)

HEC.12: 23 residues within 4Å: Chain G: V.119, V.123, C.124, C.127, H.128, N.192, A.195, L.196, P.197, P.198, L.200, I.203, R.207, Y.213, L.217, L.218, F.241, I.246, G.247, M.248, T.251, V.274, L.278 25 PLIP interactions: 25 interactions with chain G, Hydrophobic interactions: G:V.119, G:V.123, G:N.192, G:A.195, G:P.197, G:P.197, G:P.198, G:L.200, G:I.203, G:L.217, G:L.218, G:L.218, G:F.241, G:I.246, G:M.248, G:T.251, G:V.274, G:L.278 Hydrogen bonds: G:Y.213, G:Y.213, G:G.247 Water bridges: G:R.207, G:R.207 Salt bridges: G:R.207 Metal complexes: G:H.128 HEC.27: 23 residues within 4Å: Chain Q: V.119, V.123, C.124, C.127, H.128, N.192, A.195, L.196, P.197, P.198, L.200, I.203, R.207, Y.213, L.217, L.218, F.241, I.246, G.247, M.248, T.251, V.274, L.278 25 PLIP interactions: 25 interactions with chain Q, Hydrophobic interactions: Q:V.119, Q:V.123, Q:N.192, Q:A.195, Q:P.197, Q:P.197, Q:P.198, Q:L.200, Q:I.203, Q:L.217, Q:L.218, Q:L.218, Q:F.241, Q:I.246, Q:M.248, Q:T.251, Q:V.274, Q:L.278 Hydrogen bonds: Q:Y.213, Q:Y.213, Q:G.247 Water bridges: Q:R.207, Q:R.207 Salt bridges: Q:R.207 Metal complexes: Q:H.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wieferig, J.P. et al., Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III 2 by cryo-EM. Iucrj (2023)

Release Date

2023-01-11

Peptides

Cytochrome b: AK
Cytochrome b-c1 complex subunit Rieske, mitochondrial: BL
Cytochrome b-c1 complex subunit 7: CM
YALI0F24673p: DN
YALI0A14806p: EO
Cytochrome b-c1 complex subunit 2, mitochondrial: FP
YALI0A17468p: GQ
Cytochrome b-c1 complex subunit 8: HR
Complex III subunit 9: IS
YALI0C12210p: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

K
N

B
P

L
E

C
G

M
R

D
F

N
Q

E
A

O
L

F
B

P
M

G
D

Q
O

H
H

R
S

I
I

S
T

J
J

T
U

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Cytochrome b

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

YALI0F24673p

YALI0A14806p

Cytochrome b-c1 complex subunit 2, mitochondrial

YALI0A17468p

Cytochrome b-c1 complex subunit 8

Complex III subunit 9

YALI0C12210p

Related Entries With Identical Sequence