SMTL ID : 7nyv.1

Respiratory complex I from Escherichia coli - conformation 3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: C.63, C.64, G.100, T.101, A.128, C.129, C.158 Chain B: R.250, R.270, H.355 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.63, A:C.64, A:C.129, A:C.158 SF4.3: 12 residues within 4Å: Chain D: I.179, P.197, S.350, C.351, G.352, W.353, C.354, C.357, T.396, F.397, C.398, H.400 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.351, D:C.354, D:C.357, D:C.398 SF4.6: 12 residues within 4Å: Chain E: C.151, I.152, A.153, C.154, Y.155, R.156, C.157, F.181, C.201, T.203, V.205, F.206 5 PLIP interactions: 5 interactions with chain E, pi-Cation interactions: E:F.181 Metal complexes: E:C.151, E:C.154, E:C.157, E:C.201 SF4.7: 11 residues within 4Å: Chain B: I.512 Chain E: H.99, D.102, C.103, C.106, G.109, C.112, L.114, Q.115, T.203, G.204 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:H.99, E:C.103, E:C.106, E:C.112 SF4.8: 8 residues within 4Å: Chain E: C.228, Q.230, C.231, I.233, C.235, C.263, G.266, R.388 7 PLIP interactions: 7 interactions with chain E, Metal complexes: E:C.228, E:C.228, E:C.231, E:C.235, E:C.235, E:C.263, E:C.263 SF4.10: 13 residues within 4Å: Chain F: C.60, V.61, A.62, C.63, N.64, C.66, L.77, F.92, C.109, P.110, T.111, A.113, I.114 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.60, F:C.63, F:C.66, F:C.109 SF4.11: 12 residues within 4Å: Chain F: I.48, C.70, P.71, V.72, C.74, I.75, C.99, I.100, F.101, C.102, G.103, C.105 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.70, F:C.99, F:C.102, F:C.105

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

FES.2: 9 residues within 4Å: Chain C: C.92, S.94, V.96, C.97, C.133, L.134, G.135, C.137, N.142 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.92, C:C.97, C:C.133, C:C.137 FES.5: 9 residues within 4Å: Chain E: C.34, W.35, A.44, C.45, R.46, Q.47, C.48, M.65, C.67 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.34, E:C.45, E:C.48, E:C.67

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 18 residues within 4Å: Chain D: G.61, R.62, G.63, K.72, N.90, E.93, M.94, Y.178, I.179, G.181, E.182, E.183, V.216, N.217, N.218, T.221, A.399, H.400 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Y.178, D:Y.178, D:I.179, D:E.182, D:E.182, D:A.399, D:H.400 Hydrogen bonds: D:R.62, D:G.63, D:N.90, D:E.93, D:E.93, D:E.93, D:M.94, D:G.181, D:E.183, D:N.218, D:N.218, D:T.221 Salt bridges: D:K.72

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain E: D.617, Q.632, E.647, D.731 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.617, E:E.647, E:D.731

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolata, P. et al., Structure of Escherichia coli respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation. Elife (2021)

Release Date

2021-08-25

Peptides

NADH-quinone oxidoreductase subunit B: A
NADH-quinone oxidoreductase subunit C/D: B
NADH-quinone oxidoreductase subunit E: C
NADH-quinone oxidoreductase subunit F: D
NADH-quinone oxidoreductase subunit G: E
NADH-quinone oxidoreductase subunit I: F
NADH-quinone oxidoreductase subunit K: G
NADH-quinone oxidoreductase subunit J: H
NADH-quinone oxidoreductase subunit A: I
NADH-quinone oxidoreductase subunit H: J
NADH-quinone oxidoreductase subunit M: K
NADH-quinone oxidoreductase subunit L: L
NADH-quinone oxidoreductase subunit N: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

D
F

E
G

F
I

G
K

H
J

I
A

J
H

K
M

L
L

M
N

Membrane

We predict this structure to be a membrane protein.
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NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit C/D

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit F

NADH-quinone oxidoreductase subunit G

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase subunit J

NADH-quinone oxidoreductase subunit A

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit M

NADH-quinone oxidoreductase subunit L

NADH-quinone oxidoreductase subunit N

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