SMTL ID : 7ard.1

Cryo-EM structure of Polytomella Complex-I (complete composition)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-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: 13 residues within 4Å: Chain 1: X.11, X.14 Chain A: A.135, V.138, G.139, F.141, F.142, W.145, R.146 Chain H: P.279 Chain N: I.19, I.23 Chain n: N.6 9 PLIP interactions: 7 interactions with chain A, 1 interactions with chain N, 1 interactions with chain n Hydrophobic interactions: A:F.141, A:F.142, A:F.142, A:W.145, A:W.145, A:W.145, N:I.19 Salt bridges: A:R.146 Hydrogen bonds: n:N.6 PC7.13: 25 residues within 4Å: Chain 7: L.45, Y.46 Chain L: S.160, K.163, S.164, N.166, K.167, I.170, F.223, F.224, D.230, E.233, Y.509, C.513, S.514, F.517, Y.518 Chain M: F.264, F.389, F.391, V.395, T.399 Chain b: I.59, Y.60, D.61 21 PLIP interactions: 4 interactions with chain M, 12 interactions with chain L, 3 interactions with chain b, 2 interactions with chain 7 Hydrophobic interactions: M:F.264, M:F.389, M:F.391, M:V.395, L:K.167, L:I.170, L:F.224, L:F.224, L:Y.509, L:Y.509, L:F.517, L:Y.518, b:Y.60, 7:L.45, 7:Y.46 Salt bridges: L:K.163, L:K.167, L:D.230, L:E.233, b:D.61 Hydrogen bonds: b:D.61 PC7.17: 26 residues within 4Å: Chain 2: Y.41 Chain L: F.10, I.14, G.17, F.18, L.113, S.116, Y.117, A.120, F.124, I.127, G.143, V.146, L.150, Y.154 Chain M: S.339, Q.340, W.346, S.347, V.350, F.351, F.359, P.360, L.361, K.405 Ligands: PC7.18 17 PLIP interactions: 11 interactions with chain L, 6 interactions with chain M Hydrophobic interactions: L:F.10, L:F.10, L:F.18, L:F.18, L:F.18, L:Y.117, L:Y.117, L:F.124, L:I.127, M:V.350, M:F.351, M:F.359, M:L.361 Hydrogen bonds: L:Y.117, M:S.339 pi-Cation interactions: L:Y.154 Salt bridges: M:K.405 PC7.18: 19 residues within 4Å: Chain 2: F.72 Chain 6: Y.82, Y.83 Chain L: V.6, Y.7, F.10, I.14, F.18, L.61, F.62, E.63, N.64, F.65, I.127, M.136 Chain M: I.435, G.436, Y.437 Ligands: PC7.17 11 PLIP interactions: 8 interactions with chain L, 2 interactions with chain M, 1 interactions with chain 6 Hydrophobic interactions: L:V.6, L:F.10, L:I.14, L:F.18, L:F.18, L:L.61, L:L.61, L:I.127 Hydrogen bonds: M:Y.437, 6:Y.83 pi-Cation interactions: M:Y.437 PC7.20: 18 residues within 4Å: Chain 3: L.50 Chain 5: M.60, L.64 Chain N: 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 Ligands: CDL.19, CDL.27 13 PLIP interactions: 1 interactions with chain 3, 11 interactions with chain N, 1 interactions with chain 5 Hydrophobic interactions: 3:L.50, N:Y.33, N:K.36, N:I.40, N:V.44, N:W.56, N:L.64, N:W.359, N:W.359, N:W.359, 5:L.64 Hydrogen bonds: N:Y.33 Salt bridges: N:K.36 PC7.21: 18 residues within 4Å: Chain 5: Y.18 Chain A: E.124, Y.125, W.128, V.129, T.132, A.135 Chain J: S.126, D.127, L.130, L.131 Chain N: M.1, N.4, Y.7, L.8, L.11, I.12, F.84 16 PLIP interactions: 2 interactions with chain J, 7 interactions with chain N, 6 interactions with chain A, 1 interactions with chain 5 Hydrophobic interactions: J:L.130, J:L.131, N:M.1, N:L.8, N:L.8, N:L.11, N:I.12, N:F.84, N:F.84, A:Y.125, A:Y.125, A:W.128, A:W.128, A:W.128, A:A.135, 5:Y.18 PC7.32: 16 residues within 4Å: Chain 5: V.59, Y.62, Y.63, A.66 Ligands: CDL.27 Chain n: H.17, I.24, E.25, V.27, L.28, L.31 Chain o: L.26, K.29, L.30, Q.31, G.32 12 PLIP interactions: 7 interactions with chain n, 3 interactions with chain 5, 2 interactions with chain o Hydrophobic interactions: n:I.24, n:V.27, n:L.28, n:L.31, 5:Y.62, 5:Y.62, 5:Y.63, o:L.26, o:L.26 Hydrogen bonds: n:S.10 Salt bridges: n:H.17, n:E.25

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 12 residues within 4Å: Chain B: A.38, C.39, C.40, G.75, T.76, S.103, C.104, G.133, C.134, P.135 Chain D: R.70, H.155 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.39, B:C.40, B:C.104, B:C.134 SF4.5: 14 residues within 4Å: Chain F: I.213, P.231, S.386, C.387, G.388, Q.389, C.390, C.393, R.394, T.431, I.432, C.433, L.435, G.436 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.387, F:C.390, F:C.393, F:C.433 SF4.7: 9 residues within 4Å: Chain G: H.136, D.139, C.140, C.143, Q.145, G.146, C.149, Q.152, V.240 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.136, G:C.140, G:C.143, G:C.149 SF4.8: 10 residues within 4Å: Chain G: C.188, I.189, C.191, C.194, V.218, C.238, P.239, V.240, A.242, L.243 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.188, G:C.191, G:C.194, G:C.238 SF4.10: 12 residues within 4Å: Chain I: H.118, C.140, P.141, I.145, C.169, I.170, Y.171, C.172, G.173, F.174, C.175, E.186 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.186 Metal complexes: I:C.140, I:C.169, I:C.172, I:C.175 SF4.11: 12 residues within 4Å: Chain I: C.130, I.131, S.132, C.133, K.134, C.136, I.147, Y.162, C.179, V.181, A.183, I.184 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.130, I:C.133, I:C.136, I:C.179

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

FES.3: 10 residues within 4Å: Chain E: C.143, T.145, P.147, C.148, C.184, M.185, G.186, A.187, C.188 Chain F: P.130 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.143, E:C.148, E:C.184, E:C.188 FES.6: 9 residues within 4Å: Chain G: R.74, C.76, Y.77, G.85, N.86, C.87, R.88, C.90, C.104 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.76, G:C.87, G:C.90, G:C.104

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 20 residues within 4Å: Chain F: G.95, R.96, G.97, A.99, K.106, N.124, D.126, E.127, S.128, Y.212, I.213, G.215, E.216, E.217, V.250, T.251, N.252, T.255, A.434, L.435 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:Y.212, F:Y.212, F:I.213, F:E.216, F:E.216, F:A.434, F:L.435 Hydrogen bonds: F:R.96, F:N.124, F:D.126, F:D.126, F:G.215, F:N.252 Salt bridges: F:K.106

7 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.9: 20 residues within 4Å: Chain D: R.198 Chain H: P.176, L.179, Y.182, I.183, L.186, P.193, F.194, V.257, L.261, Y.264, I.272, S.276, L.277, V.280, L.284 Chain I: V.75, V.77, L.78, L.80 18 PLIP interactions: 14 interactions with chain H, 2 interactions with chain I, 2 interactions with chain D Hydrophobic interactions: H:L.179, H:Y.182, H:Y.182, H:I.183, H:P.193, H:F.194, H:V.257, H:L.261, H:I.272, H:L.277, H:V.280, H:L.284, I:V.75, I:L.78 Hydrogen bonds: H:Y.264, D:R.198 Water bridges: H:S.276 Salt bridges: D:R.198 PTY.14: 15 residues within 4Å: Chain 7: E.37 Chain L: L.222, F.223, G.503, G.504, F.505, F.508, K.512 Chain b: L.73, E.74, M.76, A.77, W.80, L.81, L.84 16 PLIP interactions: 9 interactions with chain L, 6 interactions with chain b, 1 interactions with chain 7 Hydrophobic interactions: L:L.222, L:F.223, L:F.505, L:F.505, L:F.508, L:F.508, L:F.508, b:M.76, b:W.80, b:W.80, b:L.81, b:L.84 Water bridges: L:R.511, b:L.73 Salt bridges: L:K.512 Hydrogen bonds: 7:E.37 PTY.15: 22 residues within 4Å: Chain 6: F.74, F.75, L.76, A.78, F.79, Y.82, V.90, I.91, P.92 Chain L: Y.67 Chain M: W.42, Y.69, L.72, Y.73, L.76, F.80, Q.300, A.429, V.432, Y.437, M.438 Chain Y: Y.5 25 PLIP interactions: 11 interactions with chain 6, 13 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: 6:F.74, 6:F.74, 6:F.75, 6:F.75, 6:F.75, 6:L.76, 6:F.79, 6:F.79, 6:Y.82, 6:Y.82, M:W.42, M:W.42, M:W.42, M:L.72, M:Y.73, M:L.76, M:L.76, M:F.80, M:A.429, M:V.432 Water bridges: 6:S.93, M:Q.300 Hydrogen bonds: M:Y.73, M:Q.300, L:Y.67 PTY.22: 22 residues within 4Å: Chain L: L.535 Chain M: S.141, Y.144, N.145, I.148, Y.149, I.152, F.201 Chain N: W.222, Y.229, F.320, S.321, L.324, T.327, I.328, I.331, R.335 Chain O: Y.97, Y.98, D.125 Ligands: CDL.12, CDL.31 17 PLIP interactions: 9 interactions with chain N, 7 interactions with chain M, 1 interactions with chain O Hydrophobic interactions: N:W.222, N:W.222, N:F.320, N:F.320, N:T.327, N:I.328, N:I.331, M:I.148, M:Y.149, M:Y.149, M:I.152, M:F.201, M:F.201 Hydrogen bonds: N:Y.229, O:Y.98 Salt bridges: N:R.335 Water bridges: M:N.145 PTY.26: 14 residues within 4Å: Chain M: F.186, F.201 Chain Y: K.123, S.125, Y.126, T.127, M.130, L.154, A.158, V.161, I.162 Ligands: CDL.12, PTY.28 Chain c: F.122 8 PLIP interactions: 7 interactions with chain Y, 1 interactions with chain M Hydrophobic interactions: Y:Y.126, Y:L.154, Y:I.162, M:F.201 Hydrogen bonds: Y:S.125, Y:Y.126, Y:T.127, Y:T.127 PTY.28: 22 residues within 4Å: Chain M: I.159, S.160, S.182, F.183, V.184, A.185, F.186, G.187, F.189, W.193, S.243, A.247, L.250, I.251 Chain Y: Y.126, L.165, F.166, Y.170 Ligands: PTY.26 Chain c: Y.121, F.122, D.124 22 PLIP interactions: 13 interactions with chain M, 5 interactions with chain Y, 4 interactions with chain c Hydrophobic interactions: M:I.159, M:F.183, M:F.183, M:V.184, M:A.185, M:F.186, M:F.186, M:F.189, M:W.193, M:L.250, M:L.250, M:I.251, Y:L.165, Y:L.165, Y:F.166, Y:Y.170, c:Y.121, c:Y.121, c:F.122 Hydrogen bonds: M:S.182, Y:Y.126, c:F.122 PTY.29: 17 residues within 4Å: Chain 7: Y.43, Y.46, I.53, F.54, L.57, N.61 Chain M: L.256, A.385 Chain c: G.93, L.94, V.96, A.97, M.98, A.100, T.101, F.104, R.107 9 PLIP interactions: 4 interactions with chain 7, 2 interactions with chain M, 3 interactions with chain c Hydrophobic interactions: 7:Y.46, 7:I.53, 7:F.54, M:L.256, M:A.385, c:L.94, c:T.101 Hydrogen bonds: 7:N.61 Salt bridges: c:R.107

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 26 residues within 4Å: Chain L: L.528, F.532, L.533, K.534, L.535, Y.536 Chain M: Y.149, P.200, F.201 Chain Y: P.147, V.151, L.154, V.155, A.158 Ligands: PTY.22, PTY.26, CDL.31 Chain c: W.79, L.87, Y.95 Chain i: I.9, H.10, W.11, R.12 Chain j: L.114, S.117 17 PLIP interactions: 4 interactions with chain L, 4 interactions with chain i, 2 interactions with chain j, 2 interactions with chain M, 3 interactions with chain Y, 2 interactions with chain c Hydrophobic interactions: L:L.528, L:F.532, j:L.114, j:L.114, M:P.200, M:F.201, Y:L.154, Y:V.155, Y:V.155, c:W.79, c:Y.95 Hydrogen bonds: L:Y.536, i:H.10, i:R.12 Water bridges: L:L.535 Salt bridges: i:R.12, i:R.12 CDL.16: 34 residues within 4Å: Chain 3: Y.9, L.12, C.13, M.15, V.16, I.19, G.20, V.23, I.24 Chain M: P.12, L.13, L.15, S.16, F.17, R.20, Y.92, R.93, S.96, C.100, L.120, S.123, L.126, L.127, I.130 Chain N: F.282, A.285, I.286, F.297, Y.341, N.358, T.361, W.362, T.365 Chain d: L.120 23 PLIP interactions: 8 interactions with chain M, 7 interactions with chain 3, 8 interactions with chain N Hydrophobic interactions: M:F.17, M:L.126, M:L.127, 3:Y.9, 3:L.12, 3:M.15, 3:V.16, 3:V.16, 3:I.19, N:F.282, N:A.285, N:I.286, N:F.297, N:T.361, N:W.362 Hydrogen bonds: M:Y.92, 3:V.23 Salt bridges: M:R.20, M:R.93, M:R.93, M:R.93 Water bridges: N:K.281, N:F.282 CDL.19: 29 residues within 4Å: Chain 3: L.50, V.53, Y.57, R.64 Chain 5: V.53, S.85, Y.89 Chain 8: D.47, V.73 Chain N: I.41, V.44, G.45, V.47, Y.48, D.49, I.50, P.51, A.53, I.54, W.56, C.57, S.258, W.259, F.262, S.263, L.298, M.363, M.371 Ligands: PC7.20 22 PLIP interactions: 12 interactions with chain N, 8 interactions with chain 3, 1 interactions with chain 5, 1 interactions with chain 8 Hydrophobic interactions: N:I.41, N:V.47, N:I.50, N:I.50, N:A.53, N:I.54, N:W.56, N:W.259, N:F.262, N:F.262, 3:L.50, 3:V.53, 3:V.53, 3:Y.57, 3:Y.57, 5:Y.89 Hydrogen bonds: N:D.49, N:I.50, 3:Y.57, 3:R.64, 3:R.64, 8:D.47 CDL.27: 30 residues within 4Å: Chain 3: G.10, C.13, Y.17, R.32, P.33, W.34, V.35, V.37, T.38, S.39, L.42, G.46, S.47, L.50 Chain 5: Y.63, K.67 Chain N: W.359, W.362, V.366, P.370 Ligands: PC7.20, PC7.32 Chain n: F.35, M.42 Chain o: A.15, T.19, A.22, L.23, L.26, K.29 14 PLIP interactions: 5 interactions with chain 3, 3 interactions with chain N, 4 interactions with chain o, 1 interactions with chain 5, 1 interactions with chain n Hydrophobic interactions: 3:Y.17, 3:P.33, 3:W.34, 3:L.50, N:W.362, N:V.366, N:P.370, o:T.19, o:A.22, o:L.26, n:F.35 Salt bridges: 3:R.32, o:K.29, 5:K.67 CDL.31: 38 residues within 4Å: Chain N: A.171, P.172, H.174, M.175, W.215, I.219, W.222, L.223, I.226, S.227, Q.230, Y.240 Chain Y: V.62, L.65, H.69, F.72, V.155 Ligands: CDL.12, PTY.22 Chain i: L.5, W.11 Chain j: Y.83, Y.84, Y.86, V.87, F.90, G.91, F.94, L.109, A.113, L.114, G.116, S.117, L.118, Y.120, R.122, R.123, D.124 34 PLIP interactions: 20 interactions with chain j, 3 interactions with chain Y, 10 interactions with chain N, 1 interactions with chain i Hydrophobic interactions: j:Y.83, j:Y.86, j:F.90, j:F.94, j:A.113, j:L.114, j:L.118, j:Y.120, j:Y.120, j:Y.120, j:R.122, Y:V.62, Y:L.65, Y:V.155, N:W.215, N:I.219, N:I.219, N:W.222, N:L.223, N:I.226, i:L.5 Hydrogen bonds: j:Y.84, j:Y.84, j:Y.120, j:R.123, j:D.124, N:Q.230, N:Y.240 Salt bridges: j:R.122, j:R.122, j:R.123, j:R.123, N:H.174 Water bridges: N:Q.230

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.23: 26 residues within 4Å: Chain B: K.164 Chain P: G.34, N.36, G.37, F.38, I.39, R.59, N.61, F.83, I.85, C.104, V.105, G.106, I.107, R.108, Y.114, V.119, V.143, S.144, E.145, R.156, K.160, P.179, G.180, V.182, Y.188 28 PLIP interactions: 23 interactions with chain P, 5 interactions with chain B Hydrophobic interactions: P:P.179, P:V.182 Hydrogen bonds: P:G.34, P:N.36, P:N.36, P:G.37, P:F.38, P:I.39, P:N.61, P:G.106, P:R.156, P:K.160, P:V.182, P:Y.188 Water bridges: P:G.40, P:R.59, P:R.59, P:I.85, P:E.145, P:R.156, B:K.164, B:K.164, B:K.164, B:K.164 Salt bridges: P:R.59, P:R.108, B:K.164 pi-Cation interactions: P:R.59

1 x ZN: ZINC ION(Non-covalent)

ZN.24: 5 residues within 4Å: Chain R: S.85, G.87, C.95, C.113, T.116 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:S.85, R:C.113

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

8Q1.25: 20 residues within 4Å: Chain U: D.79, S.80, L.81 Chain W: C.20, Q.21, A.23, R.24, L.26, I.37, K.59, F.60, N.63, S.64, V.66, T.72, L.75, G.79, E.82, Y.86, Y.100 12 PLIP interactions: 10 interactions with chain W, 2 interactions with chain U Hydrophobic interactions: W:I.37, W:K.59, W:F.60, W:F.60, W:T.72, W:Y.86, W:Y.100 Hydrogen bonds: W:C.20, W:R.24, W:N.63, U:S.80, U:S.80 8Q1.30: 20 residues within 4Å: Chain T: D.79, S.80, L.81 Chain d: H.11, K.12, V.15, M.18, E.25, L.43, E.46, F.47, N.50, K.51, L.53, I.59, V.63, G.66, L.70 Chain i: I.50, L.54 16 PLIP interactions: 11 interactions with chain d, 2 interactions with chain i, 3 interactions with chain T Hydrophobic interactions: d:V.15, d:V.15, d:E.25, d:L.43, d:F.47, d:I.59, d:L.70, i:L.54, i:L.54 Hydrogen bonds: d:N.50, d:K.51, T:S.80, T:S.80, T:L.81 Salt bridges: d:K.12, d: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
PSST: B
ND9: C
ND7: D
24 kDa: E
51 kDa: F
75 kDa: G
ND1: H
TYKY: I
ND6: J
ND4L: K
ND5: L
ND4: M
ND2: N
C1-FDX: O
39 kDa: P
18 kDa: Q
13 kDa: R
B8: S
SDAP1: T
SDAP2: U
B13: V
B14: W
PGIV: X
B14.7: Y
B16.6: Z
MWFE: 0
B9: 1
KFYI: 2
B14.5b: 3
15 kDa: 4
MNLL: 5
ESSS: 6
NUOP4: 7
NUOP5: 8
AGGG: 9
B12: a
ASHI: b
B15: c
Complex I-B22: d
B18: e
PDSW: f
B17.2: g
B14.5a: h
NUOP7: i
NUOP8: j
unknown: k
unknown: l
CAL: m
CA2: n
CA3: o

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
o

f
p

g
q

h
r

i
s

j
t

k
u

l
w

m
x

n
y

o
z

Membrane

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

ND3

PSST

ND9

ND7

24 kDa

51 kDa

75 kDa

ND1

TYKY

ND6

ND4L

ND5

ND4

ND2

C1-FDX

39 kDa

18 kDa

13 kDa

B8

SDAP1

SDAP2

B13

B14

PGIV

B14.7

B16.6

MWFE

B9

KFYI

B14.5b

15 kDa

MNLL

ESSS

NUOP4

NUOP5

AGGG

B12

ASHI

B15

Complex I-B22

B18

PDSW

B17.2

B14.5a

NUOP7

NUOP8

unknown

unknown

CAL

CA2

CA3

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