SMTL ID : 8bef.1

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane core)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.1: 25 residues within 4Å: Chain A: I.88, D.89, L.90, F.91, W.94, S.95, M.97, A.98, L.100, F.101, T.104 Chain C: F.149, V.150, L.153, V.154, L.157 Chain G: M.12, F.16, V.19, I.23, I.26, F.138 Chain M: L.28 Chain P: M.1 Ligands: 3PH.23 19 PLIP interactions: 5 interactions with chain C, 5 interactions with chain G, 9 interactions with chain A Hydrophobic interactions: C:V.150, C:L.153, C:L.153, C:V.154, C:L.157, G:F.16, G:V.19, G:I.23, G:I.26, G:F.138, A:F.91, A:W.94, A:W.94, A:A.98, A:L.100, A:F.101, A:F.101 Hydrogen bonds: A:L.90, A:F.91 PGT.6: 10 residues within 4Å: Chain C: L.95 Chain E: W.642, S.644, L.645, W.648, S.654 Chain J: I.24, G.28, A.29, I.32 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: C:L.95, E:W.642, J:I.32 PGT.7: 8 residues within 4Å: Chain E: I.596 Chain G: L.427 Chain J: P.115, A.122, V.126 Ligands: PTY.8, PTY.11, PTY.18 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain J Hydrophobic interactions: G:L.427, J:P.115, J:V.126, J:V.126 PGT.9: 10 residues within 4Å: Chain F: F.183, L.186, L.190, F.215, A.219, A.222 Chain G: L.418, Y.423, L.427 Ligands: PTY.10 6 PLIP interactions: 1 interactions with chain G, 5 interactions with chain F Hydrophobic interactions: G:L.427, F:F.183, F:F.183, F:L.186, F:A.219, F:A.222 PGT.30: 7 residues within 4Å: Chain G: W.56 Chain P: L.50, S.51 Chain U: K.233 Ligands: PTY.16, PC7.27, PTY.31 4 PLIP interactions: 2 interactions with chain P, 1 interactions with chain U, 1 interactions with chain G Hydrophobic interactions: P:L.50, P:L.50, G:W.56 Salt bridges: U:K.233

1 x UQ9: Ubiquinone-9(Non-covalent)

UQ9.2: 13 residues within 4Å: Chain A: I.21, L.22, V.25 Chain B: A.21, V.24, R.28, P.51, D.54, G.55, L.58, F.225, F.229, L.230 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.21, A:L.22, A:V.25, B:A.21, B:V.24, B:L.58, B:L.230, B:L.230 Hydrogen bonds: B:R.28

10 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.3: 15 residues within 4Å: Chain B: F.184, P.185, L.187, V.188, M.189, F.191, L.279, Y.290, L.298, V.302, F.303, L.306, W.310 Chain K: V.53, S.54 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.184, B:P.185, B:L.187, B:V.188, B:F.191, B:L.306, B:W.310, B:W.310 PTY.8: 9 residues within 4Å: Chain E: T.605, L.609, F.662, Y.663 Chain J: A.119, T.123, V.126 Ligands: PGT.7, PTY.13 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain E Hydrophobic interactions: J:A.119, J:T.123, J:V.126, E:L.609, E:F.662 PTY.10: 5 residues within 4Å: Chain F: I.214, I.218, F.221 Ligands: PGT.9, PTY.11 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:I.218, F:F.221 PTY.11: 17 residues within 4Å: Chain E: P.599, I.602, S.603, R.607 Chain F: K.168, Y.171, Q.172, L.175, Y.176, L.179 Chain G: M.310, V.434, F.438, R.442, K.445 Ligands: PGT.7, PTY.10 11 PLIP interactions: 5 interactions with chain F, 2 interactions with chain E, 4 interactions with chain G Hydrophobic interactions: F:Q.172, F:Y.176, F:Y.176, F:L.179, E:P.599, E:I.602, G:V.434, G:F.438, G:F.438 Hydrogen bonds: F:Y.171, G:R.442 PTY.13: 16 residues within 4Å: Chain E: L.616, F.655 Chain G: F.295, F.296, I.299, A.300, I.303, C.420, G.421, A.422, F.424 Chain J: V.126, T.127, L.130 Ligands: PTY.8, UQ5.19 10 PLIP interactions: 6 interactions with chain G, 2 interactions with chain E, 2 interactions with chain J Hydrophobic interactions: G:F.296, G:I.299, G:A.300, G:I.303, G:F.424, E:L.616, E:F.655, J:V.126, J:L.130 Hydrogen bonds: G:C.420 PTY.14: 16 residues within 4Å: Chain F: R.73 Chain G: F.350, F.475, L.478, F.479, L.481, Y.482, L.486 Chain N: A.5, F.45, A.46, L.49, V.50 Ligands: Q7G.12, PTY.15, PTY.16 15 PLIP interactions: 10 interactions with chain G, 4 interactions with chain N, 1 interactions with chain F Hydrophobic interactions: G:F.350, G:F.475, G:F.475, G:L.478, G:F.479, G:L.481, G:L.481, G:Y.482, G:L.486, N:F.45, N:A.46, N:L.49 Hydrogen bonds: G:Y.482, N:A.5, F:R.73 PTY.15: 21 residues within 4Å: Chain G: A.70, A.73, N.91, Y.94, F.95, C.96, I.98, F.99, I.271, L.346, I.349, F.350, L.354, M.493 Chain N: F.45, Q.48, L.49, W.52 Ligands: PTY.14, PTY.16, PC7.24 20 PLIP interactions: 13 interactions with chain G, 7 interactions with chain N Hydrophobic interactions: G:F.95, G:F.95, G:I.98, G:F.99, G:F.99, G:F.99, G:I.271, G:L.346, G:I.349, G:I.349, G:F.350, G:F.350, G:L.354, N:F.45, N:L.49, N:W.52, N:W.52, N:W.52, N:W.52 Salt bridges: N:K.55 PTY.16: 21 residues within 4Å: Chain G: W.56, L.102, A.105, G.106, S.109, M.357, R.463, N.464, L.467, M.471, F.474, F.475 Chain N: T.16, Q.17, E.34, G.38 Ligands: PTY.14, PTY.15, PC7.24, PGT.30, PTY.31 9 PLIP interactions: 6 interactions with chain G, 1 interactions with chain P, 2 interactions with chain N Hydrophobic interactions: G:A.105, G:N.464, G:L.467, G:F.474, N:T.16, N:E.34 Salt bridges: G:R.463, G:R.463 Water bridges: P:K.54 PTY.18: 5 residues within 4Å: Chain E: L.597 Chain J: I.114, P.115, I.118 Ligands: PGT.7 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: J:I.114, J:I.118, E:L.597 PTY.31: 18 residues within 4Å: Chain G: R.463 Chain N: H.31, W.33, E.34, V.36, V.37 Chain T: P.237, Y.238 Chain U: L.22 Chain V: T.18, A.21, L.22, R.24, L.25, R.28 Ligands: PTY.16, PC7.27, PGT.30 18 PLIP interactions: 6 interactions with chain N, 10 interactions with chain V, 1 interactions with chain T, 1 interactions with chain U Hydrophobic interactions: N:W.33, N:V.36, N:V.36, V:T.18, V:L.22, V:L.25, U:L.22 Water bridges: N:R.30, N:H.31, N:H.31, V:R.24, V:R.24, V:R.24, V:R.24, V:R.28 Salt bridges: V:R.24, V:R.28 Hydrogen bonds: T:Y.238

4 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.4: 17 residues within 4Å: Chain B: D.95, Y.96, M.172, W.251, L.252, P.264, S.266 Chain I: C.81, Y.84, Y.85, L.91 Chain L: G.17, I.21, N.24, Y.27, Y.28, K.31 12 PLIP interactions: 6 interactions with chain B, 2 interactions with chain L, 4 interactions with chain I Hydrogen bonds: B:D.95, B:G.265, L:K.31, L:K.31, I:Y.84, I:Y.85, I:Y.85, I:Y.85 Water bridges: B:Y.96, B:Y.96, B:W.251, B:S.266 Q7G.5: 19 residues within 4Å: Chain A: F.5, I.8, F.9, L.12 Chain B: Y.109, I.113, L.116 Chain C: I.2, G.39, L.42, L.43, L.54 Chain D: D.2 Chain K: G.136, E.137, W.143 Chain L: R.51, K.54 Ligands: CDL.25 15 PLIP interactions: 1 interactions with chain L, 3 interactions with chain B, 3 interactions with chain C, 3 interactions with chain K, 1 interactions with chain D, 4 interactions with chain A Salt bridges: L:R.51 Hydrophobic interactions: B:Y.109, B:I.113, B:L.116, C:I.2, C:L.42, C:L.43, K:W.143, A:F.5, A:I.8, A:F.9, A:F.9 Hydrogen bonds: K:G.136, K:E.137, D:D.2 Q7G.12: 15 residues within 4Å: Chain F: L.72, R.73, W.74, F.82, L.140, L.141, V.144, F.145 Chain G: F.407, C.408, F.411, L.480, L.481, F.487 Ligands: PTY.14 14 PLIP interactions: 9 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:W.74, F:W.74, F:W.74, F:W.74, F:F.82, F:L.140, F:V.144, F:V.144, F:F.145, G:F.411, G:L.480, G:L.480, G:L.480, G:F.487 Q7G.20: 6 residues within 4Å: Chain B: I.3, A.4, A.7, L.10 Chain L: A.32, Y.33 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.4, B:A.7, B:L.10

1 x FE: FE (III) ION(Non-covalent)

FE.17: 4 residues within 4Å: Chain H: H.83, C.91, C.95, C.135 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.83, H:C.91, H:C.95, H:C.135, H2O.20

1 x UQ5: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE(Non-covalent)

UQ5.19: 13 residues within 4Å: Chain E: R.612, L.616, A.627, L.630 Chain G: V.244, P.245, H.247, M.248, F.296, C.297 Chain J: W.40, K.41 Ligands: PTY.13 10 PLIP interactions: 4 interactions with chain G, 2 interactions with chain J, 4 interactions with chain E Hydrophobic interactions: G:V.244, G:P.245, G:P.245, G:F.296, J:W.40, J:W.40, E:L.616, E:A.627, E:L.630 Hydrogen bonds: E:R.612

3 x PC7: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC7.21: 20 residues within 4Å: Chain F: L.27, F.28, K.117, E.118, I.121, A.122, I.125, L.129, S.148, I.151 Chain G: P.385, I.386, I.389, F.474 Chain N: L.11, L.14, M.18, A.22, L.26, Y.28 17 PLIP interactions: 3 interactions with chain G, 11 interactions with chain F, 3 interactions with chain N Hydrophobic interactions: G:I.389, G:F.474, F:L.27, F:L.27, F:F.28, F:E.118, F:I.121, F:A.122, F:I.125, F:L.129, F:I.151, F:I.151, N:L.14 Hydrogen bonds: G:I.386, N:Y.28 Salt bridges: F:K.117 pi-Cation interactions: N:Y.28 PC7.24: 14 residues within 4Å: Chain G: L.63, L.66, L.67, A.71, L.468, M.471, T.472 Chain P: R.36, Y.76, N.80, F.89 Chain S: W.99 Ligands: PTY.15, PTY.16 8 PLIP interactions: 2 interactions with chain P, 1 interactions with chain S, 5 interactions with chain G Salt bridges: P:R.36 pi-Cation interactions: P:F.89 Hydrogen bonds: S:W.99 Hydrophobic interactions: G:L.63, G:L.66, G:L.67, G:L.468, G:T.472 PC7.27: 19 residues within 4Å: Chain P: Y.49, L.50, I.53 Chain S: R.82, A.85, V.86, G.89, V.90 Chain U: I.8, V.11, W.14, I.15, T.18 Chain V: L.22, L.25, R.28, L.29 Ligands: PGT.30, PTY.31 16 PLIP interactions: 5 interactions with chain U, 5 interactions with chain S, 4 interactions with chain V, 2 interactions with chain P Hydrophobic interactions: U:I.8, U:V.11, U:W.14, U:I.15, U:I.15, S:V.86, S:V.90, V:L.22, V:L.25, V:L.25, V:L.29 Water bridges: S:D.79, S:R.82, S:R.82, P:K.58, P:K.58

2 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.22: 15 residues within 4Å: Chain A: F.101 Chain G: N.27, I.31, I.34, Y.45 Chain P: G.59, P.60, V.63, T.64, G.66, L.67, L.70, M.71 Chain S: N.81, Y.84 11 PLIP interactions: 2 interactions with chain S, 6 interactions with chain P, 2 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: S:Y.84, P:P.60, P:V.63, P:V.63, P:L.70, G:I.34, G:I.34, A:F.101 Hydrogen bonds: S:N.81 Water bridges: P:G.59, P:G.59 3PH.23: 13 residues within 4Å: Chain A: A.98, F.101, I.102 Chain G: F.13, F.16, I.23, I.26, F.30 Chain P: F.22, T.23, F.74, M.75 Ligands: PGT.1 10 PLIP interactions: 3 interactions with chain P, 4 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: P:F.22, P:F.74, G:F.16, G:I.23, G:I.26, G:F.30, A:A.98, A:F.101, A:I.102 Water bridges: P:T.23

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.25: 24 residues within 4Å: Chain B: F.71, F.72, L.73, R.75, M.76, V.79, A.80, L.84, L.116, Y.119, I.123 Chain C: V.5, H.25, L.28, F.29, I.31, L.32 Chain R: V.2, K.3, V.4, Y.7, T.11 Ligands: Q7G.5, CDL.26 30 PLIP interactions: 12 interactions with chain B, 9 interactions with chain C, 9 interactions with chain R Hydrophobic interactions: B:F.72, B:F.72, B:R.75, B:M.76, B:V.79, B:A.80, B:L.84, B:L.116, B:Y.119, B:Y.119, B:I.123, C:V.5, C:L.28, C:L.28, C:I.31, C:L.32, R:V.4, R:Y.7, R:Y.7, R:T.11 Hydrogen bonds: B:F.72, R:V.2, R:V.4 Water bridges: C:H.25, C:H.25, C:H.25, R:K.3, R:K.3 Salt bridges: C:H.25, R:K.3 CDL.26: 19 residues within 4Å: Chain C: L.15, M.16, R.19, A.20, K.21 Chain D: I.12 Chain R: V.2, K.3, L.5, T.6, F.8, G.9, M.10, L.12, A.13, A.14, A.16, F.17 Ligands: CDL.25 20 PLIP interactions: 8 interactions with chain C, 11 interactions with chain R, 1 interactions with chain D Hydrophobic interactions: C:L.15, R:L.5, R:L.5, R:T.6, R:F.8, R:L.12, R:L.12, R:F.17, R:F.17, D:I.12 Hydrogen bonds: C:K.21, R:V.2, R:K.3 Water bridges: C:N.22, C:H.25, C:H.25, C:H.25, C:H.25 Salt bridges: C:K.21, R:K.3

1 x ZN: ZINC ION(Non-covalent)

ZN.28: 4 residues within 4Å: Chain U: H.107, H.135 Chain V: H.130, Y.207 4 PLIP interactions: 2 interactions with chain U, 1 interactions with chain V, 1 Ligand-Water interactions Metal complexes: U:H.107, U:H.135, V:H.130, H2O.49

1 x BCO: Butyryl Coenzyme A(Non-covalent)

BCO.29: 21 residues within 4Å: Chain T: R.152, M.169, E.170, P.187, P.188, R.190, N.201, P.202, R.204 Chain U: Q.101, T.127, F.144, G.146, M.147, A.164, A.165, V.180, M.189, R.190, S.203, Y.207 26 PLIP interactions: 15 interactions with chain U, 9 interactions with chain T, 2 interactions with chain H Hydrophobic interactions: U:A.164, U:A.165, U:V.180, U:Y.207 Hydrogen bonds: U:Q.101, U:M.147, U:A.165, U:A.165, U:S.203, T:E.170, T:R.204, T:R.204 Water bridges: U:G.183, U:G.183, U:R.190, U:R.190, T:R.190, T:R.190, T:R.190, H:G.37, H:G.37 Salt bridges: U:R.190, U:R.190, T:R.190, T:R.190, T:R.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klusch, N. et al., Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution. Nat.Plants (2023)

Release Date

2023-01-11

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH-ubiquinone oxidoreductase chain 1: B
NADH-ubiquinone oxidoreductase chain 6: C
NADH-ubiquinone oxidoreductase chain 4L: D
NADH-ubiquinone oxidoreductase chain 5: E
NADH-ubiquinone oxidoreductase chain 4: F
NADH-ubiquinone oxidoreductase chain 2: G
AT3G07480.1: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B: I
Outer envelope pore protein 16-3, chloroplastic/mitochondrial: J
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: L
At2g46540/F11C10.23: M
Excitatory amino acid transporter: N
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B: O
At4g16450: P
P1: Q
Uncharacterized protein At1g67785: R
Uncharacterized protein At2g27730, mitochondrial: S
Gamma carbonic anhydrase-like 2, mitochondrial: T
Gamma carbonic anhydrase 2, mitochondrial: U
Gamma carbonic anhydrase 1, mitochondrial: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
J

D
K

E
L

F
M

G
N

H
O

I
X

J
Y

K
Z

L
a

M
b

N
d

O
e

P
f

Q
i

R
u

S
v

T
x

U
y

V
z

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

AT3G07480.1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B

Outer envelope pore protein 16-3, chloroplastic/mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

At2g46540/F11C10.23

Excitatory amino acid transporter

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B

At4g16450

P1

Uncharacterized protein At1g67785

Uncharacterized protein At2g27730, mitochondrial

Gamma carbonic anhydrase-like 2, mitochondrial

Gamma carbonic anhydrase 2, mitochondrial

Gamma carbonic anhydrase 1, mitochondrial

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