SMTL ID : 6rfs.1

Cryo-EM structure of a respiratory complex I mutant lacking NDUFS4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.04 Å

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-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.129, P.130, D.132, C.133, C.136, Q.138, C.142, Q.145, R.182, V.235, G.236 Chain C: I.382 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.129, A:C.133, A:C.136, A:C.142 SF4.2: 12 residues within 4Å: Chain A: C.183, I.184, H.185, C.186, T.187, R.188, C.189, C.233, P.234, V.235, A.237, L.238 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.183, A:C.186, A:C.189, A:C.233 SF4.4: 11 residues within 4Å: Chain B: P.225, S.380, C.381, G.382, Q.383, C.384, C.387, T.425, C.427, L.429, G.430 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.381, B:C.384, B:C.387, B:C.427 SF4.8: 12 residues within 4Å: Chain I: H.118, C.140, P.141, I.145, K.168, C.169, I.170, Y.171, C.172, G.173, 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 SF4.9: 12 residues within 4Å: Chain I: C.130, I.131, C.133, K.134, L.135, C.136, I.147, S.178, C.179, V.181, A.183, I.184 5 PLIP interactions: 5 interactions with chain I, Metal complexes: I:C.130, I:I.131, I:C.133, I:C.136, I:C.179 SF4.10: 10 residues within 4Å: Chain C: R.141, H.226 Chain K: C.85, C.86, G.121, T.122, G.148, S.149, C.150, C.180 5 PLIP interactions: 5 interactions with chain K, Metal complexes: K:C.85, K:C.86, K:C.150, K:C.180, K:C.180

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

FES.3: 10 residues within 4Å: Chain A: C.69, Y.70, A.77, G.78, N.79, C.80, R.81, C.83, A.95, C.97 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.69, A:C.80, A:C.83, A:C.97 FES.7: 10 residues within 4Å: Chain H: C.127, T.129, P.131, C.132, C.168, L.169, G.170, A.171, C.172, M.177 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.127, H:C.132, H:C.168, H:C.172

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 19 residues within 4Å: Chain B: G.86, R.87, G.88, A.90, K.97, N.118, D.120, E.121, G.122, E.123, G.209, E.210, E.211, V.244, T.245, N.246, T.249, A.428, L.429 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.210, B:E.210, B:A.428, B:L.429 Hydrogen bonds: B:R.87, B:G.88, B:G.88, B:N.118, B:D.120, B:G.122, B:E.123, B:G.209, B:E.211, B:N.246 Salt bridges: B:K.97

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

NDP.6: 21 residues within 4Å: Chain E: G.60, N.62, G.63, F.64, L.65, R.85, L.128, I.129, G.130, R.131, E.132, F.138, V.143, A.168, F.169, K.183, P.202, A.203, P.204, M.205, K.211 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:A.168, E:F.169, E:P.202 Hydrogen bonds: E:G.60, E:N.62, E:G.63, E:F.64, E:L.65, E:R.85, E:L.128, E:G.130, E:E.132, E:K.183, E:M.205 Salt bridges: E:R.85, E:R.131, E:K.211 pi-Cation interactions: E:R.85, E:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain M: C.97, H.110, C.125, Y.127, C.128 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:C.97, M:H.110, M:H.110, M:C.125, M:C.128

1 x ZMP: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate(Covalent)

ZMP.12: 15 residues within 4Å: Chain N: S.66, L.67 Chain O: L.21, Q.22, T.25, E.59, F.60, H.63, R.64, Q.72, L.75, Y.76, G.79, E.82, Y.99 11 PLIP interactions: 9 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: O:L.21, O:Q.22, O:E.59, O:F.60, O:Q.72, O:Y.99, N:L.67 Hydrogen bonds: O:Q.22, O:Q.72, N:S.66 Salt bridges: O:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parey, K. et al., High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease. Sci Adv (2019)

Release Date

2019-12-11

Peptides

Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I): A
Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I): B
Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I): C
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I): D
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I): E
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I): F
Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I): G
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I): H
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I): I
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I): J
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I): K
Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I): L
Subunit NUMM of NADH:Ubiquinone Oxidoreductase (Complex I): M
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I): N
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I): O
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I): P
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I): Q
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I): R
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I): S
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I): T
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I): U
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I): V
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I): W
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I): X
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I): Y
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I): Z
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I): 0
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I): 1
Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I): 2
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I): 3
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I): 4
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I): 5
Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I): 6
Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I): 7
Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I): 8
Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I): 9
Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I): a
Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I): b
Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I): c
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I): d
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I): e

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
O

O
P

P
Q

Q
R

R
S

S
U

T
W

U
X

V
Z

W
a

X
b

Y
c

Z
d

0
e

1
f

2
g

3
h

4
i

5
j

6
n

7
1

8
2

9
3

a
4

b
5

c
6

d
8

e
9

Membrane

We predict this structure to be a membrane protein.
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Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUMM of NADH:Ubiquinone Oxidoreductase (Complex I)

Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)

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