SMTL ID : 7arc.1

Cryo-EM structure of Polytomella Complex-I (peripheral 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-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: A.38, C.39, C.40, G.75, T.76, G.102, S.103, C.104, G.133, C.134, P.135 Chain C: R.70, H.155 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.39, A:C.40, A:C.104, A:C.134 SF4.4: 13 residues within 4Å: Chain E: I.213, P.231, S.386, C.387, G.388, Q.389, C.390, C.393, T.431, I.432, C.433, L.435, G.436 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.387, E:C.390, E:C.393, E:C.433 SF4.6: 11 residues within 4Å: Chain C: M.307 Chain F: H.136, P.137, D.139, C.140, C.143, Q.145, G.146, C.149, Q.152, V.240 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:H.136, F:C.140, F:C.143, F:C.149 SF4.7: 10 residues within 4Å: Chain F: M.185, C.188, I.189, C.191, C.194, V.218, C.238, V.240, A.242, L.243 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.188, F:C.191, F:C.194, F:C.238 SF4.8: 12 residues within 4Å: Chain G: 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 G, Salt bridges: G:E.186 Metal complexes: G:C.140, G:C.169, G:C.172, G:C.175 SF4.9: 12 residues within 4Å: Chain G: 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 G, Metal complexes: G:C.130, G:C.133, G:C.136, G:C.179

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

FES.2: 10 residues within 4Å: Chain D: C.143, T.145, P.147, C.148, C.184, M.185, G.186, A.187, C.188 Chain E: P.130 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.143, D:C.148, D:C.184, D:C.188 FES.5: 9 residues within 4Å: Chain F: R.74, F.75, C.76, Y.77, G.85, C.87, R.88, C.90, C.104 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.76, F:C.87, F:C.90, F:C.104

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 19 residues within 4Å: Chain E: 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, A.434, L.435 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:Y.212, E:Y.212, E:I.213, E:E.216, E:E.216, E:A.434, E:L.435 Hydrogen bonds: E:R.96, E:N.124, E:D.126, E:D.126, E:G.215, E:N.252 Salt bridges: E:K.106

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

NDP.10: 26 residues within 4Å: Chain A: K.164 Chain H: 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 27 PLIP interactions: 22 interactions with chain H, 5 interactions with chain A Hydrophobic interactions: H:P.179, H:V.182 Hydrogen bonds: H:G.34, H:N.36, H:N.36, H:F.38, H:I.39, H:N.61, H:G.106, H:R.156, H:K.160, H:V.182, H:Y.188 Water bridges: H:G.37, H:G.40, H:R.59, H:R.59, H:I.85, H:R.156, A:K.164, A:K.164, A:K.164, A:K.164 Salt bridges: H:R.59, H:R.108, A:K.164 pi-Cation interactions: H:R.59

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain J: S.85, H.86, G.87, C.95, C.113, T.116 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:S.85, J:C.95, J:C.113

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

8Q1.12: 22 residues within 4Å: Chain L: D.79, S.80, L.81 Chain N: C.20, A.23, R.24, L.26, I.37, I.56, K.59, F.60, R.61, N.63, S.64, V.66, T.72, L.75, I.76, G.79, E.82, Y.86, Y.100 12 PLIP interactions: 3 interactions with chain L, 9 interactions with chain N Hydrophobic interactions: L:L.81, N:I.37, N:F.60, N:F.60, N:T.72, N:Y.86, N:Y.100 Hydrogen bonds: L:S.80, L:S.80, N:C.20, N:R.24, N:N.63

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

PSST: A
ND9: B
ND7: C
24 kDa: D
51 kDa: E
75 kDa: F
TYKY: G
39 kDa: H
18 kDa: I
13 kDa: J
B8: K
SDAP2: L
B13: M
B14: N
B17.2: O
B14.5a: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
G

G
I

H
P

I
Q

J
R

K
S

L
U

M
V

N
W

O
q

P
r

PSST

ND9

ND7

24 kDa

51 kDa

75 kDa

TYKY

39 kDa

18 kDa

13 kDa

B8

SDAP2

B13

B14

B17.2

B14.5a

Related Entries With Identical Sequence