SMTL ID : 7ar9.1

Cryo-EM structure of Polytomella Complex-I (membrane arm)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 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)

PC7.1: 12 residues within 4Å: Chain 7: N.6 Chain A: A.135, V.138, G.139, F.141, F.142, W.145, R.146 Chain B: P.279 Chain G: I.23 Chain N: X.17, X.21 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.138, A:F.141, A:F.142, A:F.142, A:F.142, A:W.145, A:W.145 Salt bridges: A:R.146 PC7.4: 23 residues within 4Å: Chain E: F.10, I.14, G.17, F.18, S.110, L.113, S.116, Y.117, A.120, F.124, G.143, V.146, L.150, Y.154 Chain F: S.339, W.346, S.347, V.350, F.351, F.359, L.361, K.405 Chain O: Y.41 20 PLIP interactions: 14 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:F.10, E:F.10, E:F.10, E:I.14, E:F.18, E:F.18, E:L.113, E:Y.117, E:Y.117, E:A.120, E:F.124, E:V.146, F:V.350, F:F.351, F:F.351, F:F.359 Hydrogen bonds: E:Y.117, F:S.339 pi-Cation interactions: E:Y.154 Salt bridges: F:K.405 PC7.5: 22 residues within 4Å: Chain E: S.160, K.163, S.164, N.166, K.167, I.170, I.174, F.224, D.230, E.233, Y.509, C.513, F.517, Y.518 Chain F: F.264, F.391, V.395 Chain T: L.45, Y.46 Chain X: I.59, Y.60, D.61 20 PLIP interactions: 13 interactions with chain E, 3 interactions with chain X, 3 interactions with chain F, 1 interactions with chain T Hydrophobic interactions: E:K.167, E:I.170, E:I.174, E:F.224, E:F.224, E:Y.509, E:Y.509, E:F.517, E:Y.518, X:Y.60, F:F.264, F:F.391, F:V.395, T:L.45 Salt bridges: E:K.163, E:K.167, E:D.230, E:E.233, X:D.61 Hydrogen bonds: X:D.61 PC7.6: 17 residues within 4Å: Chain E: V.6, Y.7, F.10, F.18, L.61, F.62, E.63, N.64, F.65, I.127, M.136 Chain F: I.435, G.436, Y.437 Chain O: F.72 Chain S: Y.82, Y.83 11 PLIP interactions: 8 interactions with chain E, 1 interactions with chain S, 2 interactions with chain F Hydrophobic interactions: E:V.6, E:F.10, E:F.10, E:F.18, E:F.18, E:L.61, E:L.61, E:I.127 Hydrogen bonds: S:Y.83, F:Y.437 pi-Cation interactions: F:Y.437 PC7.11: 17 residues within 4Å: Chain G: Y.33, K.36, G.37, I.40, V.44, W.56, L.64, K.352, D.353, S.354, S.355, F.356, W.359 Chain R: M.60, L.64 Ligands: CDL.10, CDL.15 11 PLIP interactions: 1 interactions with chain R, 10 interactions with chain G Hydrophobic interactions: R:L.64, G:Y.33, G:K.36, G:I.40, G:V.44, G:W.56, G:W.56, G:W.359, G:W.359, G:W.359 Hydrogen bonds: G:Y.33 PC7.12: 16 residues within 4Å: Chain A: E.124, Y.125, W.128, V.129, T.132, A.135 Chain C: S.126, D.127 Chain G: M.1, N.4, Y.7, L.8, L.11, I.12, F.84 Chain R: Y.18 12 PLIP interactions: 6 interactions with chain G, 4 interactions with chain A, 1 interactions with chain C, 1 interactions with chain R Hydrophobic interactions: G:M.1, G:L.8, G:L.8, G:L.11, G:I.12, G:F.84, A:Y.125, A:W.128, A:W.128, A:A.135, C:D.127, R:Y.18 PC7.20: 17 residues within 4Å: Chain 7: H.17, P.20, I.24, E.25, V.27, L.28, L.31 Chain 8: L.26, K.29, L.30, Q.31, G.32 Chain R: V.59, Y.62, Y.63, A.66 Ligands: CDL.15 10 PLIP interactions: 5 interactions with chain 7, 1 interactions with chain 8, 4 interactions with chain R Hydrophobic interactions: 7:I.24, 7:L.28, 7:L.31, 8:L.26, R:V.59, R:Y.62, R:Y.62, R:Y.63 Salt bridges: 7:H.17, 7:E.25

7 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 11 residues within 4Å: Chain B: P.176, L.179, L.180, Y.182, L.186, V.257, L.261, I.272, S.276, V.280 Chain N: X.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.179, B:L.180, B:Y.182, B:Y.182, B:V.257, B:L.261, B:V.280 PTY.7: 15 residues within 4Å: Chain E: L.222, F.223, G.503, G.504, F.505, F.508, K.512 Chain T: E.37 Chain X: L.73, E.74, M.76, A.77, W.80, L.81, L.87 19 PLIP interactions: 1 interactions with chain T, 8 interactions with chain X, 10 interactions with chain E Hydrogen bonds: T:E.37 Hydrophobic interactions: X:M.76, X:A.77, X:W.80, X:W.80, X:L.81, X:L.81, X:L.87, E:L.222, E:F.223, E:F.505, E:F.505, E:F.508, E:F.508, E:F.508, E:F.508 Water bridges: X:L.73, E:R.511 Salt bridges: E:K.512 PTY.8: 19 residues within 4Å: Chain E: Y.67 Chain F: W.42, Y.69, L.72, Y.73, L.76, F.80, Q.300, A.429, Y.437, M.438 Chain K: Y.5 Chain S: F.75, L.76, A.78, Y.82, V.90, I.91, P.92 16 PLIP interactions: 5 interactions with chain S, 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: S:F.75, S:L.76, S:Y.82, S:Y.82, S:Y.82, F:W.42, F:Y.73, F:Y.73, F:L.76, F:F.80, F:A.429, F:Y.437, F:Y.437 Hydrogen bonds: F:Y.73, F:Q.300, E:Y.67 PTY.13: 19 residues within 4Å: Chain E: L.535 Chain F: Y.144, N.145, I.148, Y.149, F.201 Chain G: W.222, Y.229, F.320, S.321, L.324, T.327, I.331, R.335 Chain H: Y.97, Y.98, D.125 Ligands: CDL.3, PTY.14 16 PLIP interactions: 7 interactions with chain F, 8 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: F:I.148, F:I.148, F:Y.149, F:Y.149, F:F.201, F:F.201, G:W.222, G:W.222, G:F.320, G:L.324, G:T.327, G:I.331 Water bridges: F:N.145 Hydrogen bonds: G:Y.229, H:Y.98 Salt bridges: G:R.335 PTY.14: 15 residues within 4Å: Chain F: F.186, F.201 Chain K: S.125, Y.126, T.127, M.130, L.154, A.158, V.161, I.162, L.165 Chain Y: F.122 Ligands: CDL.3, PTY.13, PTY.16 12 PLIP interactions: 2 interactions with chain F, 10 interactions with chain K Hydrophobic interactions: F:F.186, F:F.201, K:L.154, K:A.158, K:I.162, K:L.165 Hydrogen bonds: K:K.123, K:K.123, K:S.125, K:Y.126, K:T.127, K:T.127 PTY.16: 18 residues within 4Å: Chain F: I.159, S.160, S.182, F.183, A.185, F.186, G.187, F.189, A.247, L.250, I.251 Chain K: F.166, Y.170, M.174 Chain Y: Y.121, F.122, D.124 Ligands: PTY.14 16 PLIP interactions: 10 interactions with chain F, 2 interactions with chain K, 4 interactions with chain Y Hydrophobic interactions: F:I.159, F:F.183, F:A.185, F:F.186, F:F.186, F:F.189, F:L.250, F:L.250, F:L.250, F:I.251, K:F.166, K:Y.170, Y:Y.121, Y:Y.121, Y:Y.121, Y:F.122 PTY.17: 15 residues within 4Å: Chain F: L.256, A.385 Chain T: Y.43, Y.46, I.53, L.57 Chain Y: A.88, G.92, G.93, V.96, A.97, A.100, T.101, R.107 Ligands: CDL.3 8 PLIP interactions: 4 interactions with chain Y, 2 interactions with chain F, 2 interactions with chain T Hydrophobic interactions: Y:A.97, Y:A.100, Y:T.101, F:L.256, F:A.385, T:Y.46, T:I.53 Salt bridges: Y:R.107

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 25 residues within 4Å: Chain 2: H.10, W.11, R.12 Chain 3: L.114, S.117 Chain E: L.528, F.532, L.533, K.534, L.535, Y.536 Chain F: Y.149, P.200, F.201 Chain K: V.151, L.154, V.155, A.158 Chain Y: W.79, A.88, Y.95 Ligands: PTY.13, PTY.14, PTY.17, CDL.19 16 PLIP interactions: 1 interactions with chain F, 5 interactions with chain E, 2 interactions with chain 3, 2 interactions with chain Y, 4 interactions with chain 2, 2 interactions with chain K Hydrophobic interactions: F:F.201, E:L.528, E:F.532, E:F.532, 3:L.114, 3:L.114, Y:W.79, Y:Y.95, K:V.155, K:A.158 Hydrogen bonds: E:Y.536, 2:H.10, 2:R.12 Water bridges: E:L.535 Salt bridges: 2:R.12, 2:R.12 CDL.9: 30 residues within 4Å: Chain F: L.13, L.15, S.16, F.17, R.20, Y.92, R.93, S.96, I.97, C.100, S.123, L.127, I.130 Chain G: F.282, A.285, F.297, Y.341, N.358, T.361, W.362, T.365 Chain P: Y.9, L.12, M.15, V.16, I.19, G.20, S.21, V.23 Chain Z: L.120 22 PLIP interactions: 9 interactions with chain F, 6 interactions with chain P, 7 interactions with chain G Hydrophobic interactions: F:L.13, F:F.17, F:I.97, F:L.127, P:Y.9, P:L.12, P:M.15, P:V.16, P:I.19, G:F.282, G:F.282, G:A.285, G:T.361, G:W.362, G:T.365 Hydrogen bonds: F:Y.92, P:V.23 Salt bridges: F:R.20, F:R.93, F:R.93, F:R.93 Water bridges: G:F.282 CDL.10: 24 residues within 4Å: Chain G: I.41, V.44, V.47, Y.48, D.49, I.50, P.51, A.53, I.54, W.56, C.57, W.259, F.262, S.263, S.266, M.363, M.371 Chain P: L.50, V.53, Y.57 Chain R: S.85, Y.89 Chain U: D.47 Ligands: PC7.11 22 PLIP interactions: 6 interactions with chain P, 1 interactions with chain R, 14 interactions with chain G, 1 interactions with chain U Hydrophobic interactions: P:L.50, P:V.53, P:V.53, P:Y.57, R:Y.89, G:I.41, G:I.41, G:V.44, G:V.47, G:I.50, G:I.50, G:I.50, G:I.54, G:W.56, G:W.259, G:W.259, G:F.262 Hydrogen bonds: P:Y.57, P:Y.57, G:D.49, G:I.50, U:D.47 CDL.15: 29 residues within 4Å: Chain 7: F.35, M.42 Chain 8: T.19, A.22, L.23, L.26, K.29 Chain G: W.359, W.362, M.363, V.366, P.370 Chain P: G.10, C.13, Y.17, R.32, P.33, W.34, V.35, T.38, S.39, L.42, S.43, G.46, S.47, L.50 Chain R: Y.63 Ligands: PC7.11, PC7.20 16 PLIP interactions: 7 interactions with chain P, 3 interactions with chain G, 1 interactions with chain R, 4 interactions with chain 8, 1 interactions with chain 7 Hydrophobic interactions: P:Y.17, P:Y.17, P:P.33, P:W.34, P:L.42, P:L.50, G:W.362, G:V.366, G:P.370, 8:T.19, 8:A.22, 8:L.26, 7:F.35 Salt bridges: P:R.32, R:K.67, 8:K.29 CDL.19: 34 residues within 4Å: Chain 2: L.5 Chain 3: Y.83, Y.84, Y.86, V.87, F.90, G.91, L.109, A.113, G.116, S.117, L.118, Y.120, R.122, R.123, D.124 Chain G: P.172, H.174, M.175, W.215, L.218, I.219, W.222, L.223, I.226, S.227, Q.230, Y.240 Chain K: V.62, L.65, A.68, H.69, F.72 Ligands: CDL.3 32 PLIP interactions: 9 interactions with chain G, 19 interactions with chain 3, 3 interactions with chain K, 1 interactions with chain 2 Hydrophobic interactions: G:P.172, G:I.219, G:W.222, G:L.223, G:I.226, 3:Y.83, 3:Y.86, 3:V.87, 3:F.90, 3:F.90, 3:A.113, 3:L.118, 3:Y.120, 3:Y.120, 3:R.122, K:V.62, K:H.69, K:F.72, 2:L.5 Hydrogen bonds: G:Q.230, G:Y.240, 3:Y.84, 3:Y.84, 3:Y.120, 3:R.123, 3:D.124 Water bridges: G:Q.230 Salt bridges: G:H.174, 3:R.122, 3:R.122, 3:R.123, 3:R.123

1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Non-covalent)

8Q1.18: 19 residues within 4Å: Chain 2: I.50, L.54 Chain I: D.79, S.80, L.81 Chain Z: H.11, K.12, V.15, M.18, I.26, L.43, E.46, F.47, N.50, K.51, L.53, I.59, G.66, L.70 15 PLIP interactions: 10 interactions with chain Z, 3 interactions with chain I, 2 interactions with chain 2 Hydrophobic interactions: Z:V.15, Z:V.15, Z:F.47, Z:F.47, Z:I.59, Z:L.70, 2:I.50, 2:L.54 Hydrogen bonds: Z:N.50, Z:K.51, I:S.80, I:S.80, I:L.81 Salt bridges: Z:K.12, Z:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klusch, N. et al., A ferredoxin bridge connects the two arms of plant mitochondrial complex I. Plant Cell (2021)

Release Date

2021-12-08

Peptides

ND3: A
ND1: B
ND6: C
ND4L: D
ND5: E
ND4: F
ND2: G
C1-FDX: H
SDAP1: I
PGIV: J
B14.7: K
B16.6: L
MWFE: M
B9: N
KFYI: O
B14.5b: P
15 kDa: Q
MNLL: R
ESSS: S
NUOP4: T
NUOP5: U
AGGG: V
B12: W
ASHI: X
B15: Y
B22: Z
B18: 0
PDSW: 1
NUOP7: 2
NUOP8: 3
unknown: 4
unknown: 5
CAL: 6
CA2: 7
CA3: 8

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
T

J
X

K
Y

L
Z

M
a

N
b

O
c

P
d

Q
e

R
f

S
g

T
h

U
i

V
j

W
k

X
l

Y
m

Z
n

0
o

1
p

2
s

3
t

4
u

5
w

6
x

7
y

8
z

Membrane

We predict this structure to be a membrane protein.
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ND3

ND1

ND6

ND4L

ND5

ND4

ND2

C1-FDX

SDAP1

PGIV

B14.7

B16.6

MWFE

B9

KFYI

B14.5b

15 kDa

MNLL

ESSS

NUOP4

NUOP5

AGGG

B12

ASHI

B15

B22

B18

PDSW

NUOP7

NUOP8

unknown

unknown

CAL

CA2

CA3

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