SMTL ID : 5xtb.1

Cryo-EM structure of human respiratory complex I matrix 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-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: I.179, P.197, S.352, C.353, G.354, Q.355, C.356, C.359, T.397, I.398, C.399, L.401 1 PLIP interactions: 1 interactions with chain A, Metal complexes: A:C.353 SF4.3: 12 residues within 4Å: Chain B: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, A.130, I.131 1 PLIP interactions: 1 interactions with chain B, Metal complexes: B:C.80 SF4.4: 13 residues within 4Å: Chain B: H.65, C.87, P.88, I.92, I.111, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 4 PLIP interactions: 4 interactions with chain B, Salt bridges: B:E.133 Metal complexes: B:C.87, B:C.116, B:C.119 SF4.5: 12 residues within 4Å: Chain C: A.30, C.31, C.32, G.67, T.68, G.94, S.95, C.96, C.126, P.127 Chain P: R.60, H.145 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.31, C:C.32, C:C.96, C:C.126 SF4.8: 11 residues within 4Å: Chain L: H.95, D.98, C.99, C.102, Q.104, G.105, C.108, L.110, Q.111, V.199, G.200 3 PLIP interactions: 3 interactions with chain L, Metal complexes: L:H.95, L:C.99, L:C.108 SF4.9: 10 residues within 4Å: Chain L: C.147, I.148, C.150, C.153, V.177, C.197, P.198, V.199, A.201, L.202 5 PLIP interactions: 5 interactions with chain L, Metal complexes: L:C.147, L:C.150, L:C.150, L:C.153, L:C.197

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 13 residues within 4Å: Chain A: G.61, R.62, G.63, N.90, D.92, E.93, Y.178, G.181, E.182, E.183, A.217, N.218, A.400 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.90, A:D.92, A:N.218 Hydrogen bonds: A:R.62, A:G.63, A:N.90, A:E.182, A:E.183, A:E.183, A:A.217, A:N.218, A:T.221, A:A.400

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

8Q1.6: 14 residues within 4Å: Chain D: M.10, V.17, L.20, W.24, V.48, M.51, F.52, N.55, A.56, V.58, V.64, L.67, V.68 Chain F: S.41 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.20, D:W.24, D:V.48, D:F.52, D:V.58, D:V.64 Hydrogen bonds: D:K.14

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

NDP.7: 22 residues within 4Å: Chain I: G.21, T.23, G.24, F.25, L.26, C.47, A.71, L.90, I.91, G.92, R.93, F.100, F.106, V.128, S.129, H.130, Y.141, K.145, P.164, D.166, I.167, R.173 16 PLIP interactions: 16 interactions with chain I Hydrophobic interactions: I:H.130, I:P.164, I:I.167 Hydrogen bonds: I:T.23, I:F.25, I:L.26, I:L.90, I:G.92, I:R.93, I:K.145, I:I.167, I:I.167 Salt bridges: I:R.93, I:R.93, I:R.173, I:R.173

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

FES.10: 10 residues within 4Å: Chain L: R.33, C.35, Y.36, A.43, N.45, C.46, R.47, M.48, C.49, C.63 1 PLIP interactions: 1 interactions with chain L, Metal complexes: L:C.46 FES.11: 9 residues within 4Å: Chain N: C.100, T.102, P.104, C.105, C.141, L.142, G.143, A.144, C.145 2 PLIP interactions: 2 interactions with chain N, Metal complexes: N:C.141, N:C.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, R. et al., Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Cell (2017)

Release Date

2017-08-30

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: E
Acyl carrier protein, mitochondrial: F
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: I
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: J
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: K
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: M
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: N
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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
T

R
W

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

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