SMTL ID : 6gcs.1

Cryo-EM structure of respiratory complex I from Yarrowia lipolytica

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.32 Å

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: H.129, P.130, D.132, C.133, C.136, Q.138, C.142, L.144, Q.145, R.182, V.235, G.236 Chain C: M.378 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.132 Metal complexes: A:H.129, A:C.133, A:C.136, A:C.142 SF4.2: 11 residues within 4Å: Chain A: C.183, I.184, H.185, C.186, T.187, 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: 13 residues within 4Å: Chain B: V.207, P.225, S.380, C.381, G.382, Q.383, C.384, C.387, T.425, I.426, 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, C.169, I.170, Y.171, C.172, G.173, Y.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 SF4.9: 11 residues within 4Å: Chain I: C.130, I.131, A.132, C.133, K.134, L.135, C.136, I.147, Y.162, C.179, A.183 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.130, I:C.133, I:C.136, I:C.179 SF4.10: 11 residues within 4Å: Chain C: R.141 Chain K: A.84, C.85, C.86, G.121, T.122, G.148, S.149, C.150, C.180, P.181 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.85, K:C.86, K:C.150, 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, M.82, C.83, 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: 9 residues within 4Å: Chain H: C.127, T.129, P.131, C.132, C.168, L.169, G.170, A.171, C.172 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: 20 residues within 4Å: Chain B: G.86, R.87, G.88, G.89, A.90, S.94, K.97, N.118, D.120, E.121, G.122, Y.206, G.209, E.210, V.244, T.245, N.246, T.249, A.428, L.429 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.206, B:E.210, B:E.210, B:A.428, B:L.429 Hydrogen bonds: B:G.88, B:A.90, B:N.118, B:D.120, B:G.122, B:N.246 Salt bridges: B:K.97

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

NDP.6: 24 residues within 4Å: Chain E: G.60, N.62, G.63, F.64, L.65, R.85, L.109, L.128, I.129, G.130, R.131, E.132, F.138, V.143, V.166, A.168, F.169, K.183, P.202, A.203, P.204, M.205, K.211 Chain K: R.209 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain K Hydrophobic interactions: E:F.169, E:F.169 Hydrogen bonds: E:N.62, E:G.63, E:F.64, E:L.65, E:R.85, E:R.85, E:I.129, E:I.129, E:E.132, E:K.183 Salt bridges: E:R.85, E:R.131, E:R.131, K:R.209 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 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.97, 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: 14 residues within 4Å: Chain N: D.65, S.66, L.67 Chain O: Q.22, T.25, F.32, E.59, F.60, H.63, R.64, Q.72, L.75, G.79, Y.99 11 PLIP interactions: 2 interactions with chain N, 9 interactions with chain O Hydrogen bonds: N:S.66, N:L.67, O:R.64 Hydrophobic interactions: O:Q.22, O:F.32, O:E.59, O:E.59, O:F.60, O:Q.72, O:Y.99 Salt bridges: O:R.64

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.13: 16 residues within 4Å: Chain 3: W.9, Y.15, F.30 Chain 9: L.4, S.8, T.11, F.12, M.15 Chain U: P.20, F.74, R.76, V.77, M.80 Ligands: 3PE.14 Chain a: L.96 Chain d: L.163 12 PLIP interactions: 4 interactions with chain U, 5 interactions with chain 3, 1 interactions with chain d, 1 interactions with chain 9, 1 interactions with chain a Hydrophobic interactions: U:V.77, U:V.77, 3:F.30, 3:F.30, 3:F.30, d:L.163, 9:F.12, a:L.96 Salt bridges: U:R.76, U:R.76 Hydrogen bonds: 3:W.9, 3:Y.15

3 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.14: 16 residues within 4Å: Chain 3: Y.15, L.16, S.19, R.23, L.26, F.27, A.29, F.30, I.34 Chain 8: P.318, L.325 Ligands: CDL.13 Chain a: I.99, V.103, I.106, N.107 13 PLIP interactions: 9 interactions with chain 3, 1 interactions with chain 8, 3 interactions with chain a Hydrophobic interactions: 3:L.16, 3:L.26, 3:F.27, 3:A.29, 3:F.30, 3:F.30, 3:F.30, 3:I.34, 8:L.325, a:I.99, a:V.103 Salt bridges: 3:R.23 Hydrogen bonds: a:N.107 3PE.15: 21 residues within 4Å: Chain 8: P.184, L.185, L.187, I.188, F.190, I.191, F.300, F.303, N.307, N.310, F.311, I.323 Chain C: R.269, L.273 Chain I: Y.77, F.78, L.80, M.83, L.87 Chain T: C.38, C.41 17 PLIP interactions: 12 interactions with chain 8, 1 interactions with chain C, 4 interactions with chain I Hydrophobic interactions: 8:P.184, 8:L.185, 8:L.187, 8:I.188, 8:F.190, 8:I.191, 8:F.300, 8:F.303, 8:F.311, 8:I.323, I:F.78, I:F.78, I:L.80, I:L.87 Hydrogen bonds: 8:N.307, 8:N.310 Salt bridges: C:R.269 3PE.16: 9 residues within 4Å: Chain 9: L.362, I.366, L.377 Chain b: S.111, N.112, L.113, T.116, P.146, L.147 6 PLIP interactions: 4 interactions with chain b, 2 interactions with chain 9 Hydrophobic interactions: b:P.146, b:L.147, 9:I.366, 9:L.377 Hydrogen bonds: b:N.112, b:T.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parey, K. et al., Cryo-EM structure of respiratory complex I at work. Elife (2018)

Release Date

2018-10-10

Peptides

75-KDA PROTEIN (NUAM): A
51-KDA PROTEIN (NUBM): B
49-KDA PROTEIN (NUCM): C
NIMM SUBUNIT: D
NUEM SUBUNIT: E
NUFM SUBUNIT: F
30-KDA PROTEIN (NUGM): G
24-KDA SUBUNIT (NUHM): H
TYKY SUBUNIT (NUIM): I
NUJM SUBUNIT: J
PSST SUBUNIT (NUKM): K
ND4L SUBUNIT (NULM): L
NUMM SUBUNIT: M
ACPM1 SUBUNIT: N
NB4M SUBUNIT: O
ACPM2 SUBUNIT: P
NI2M SUBUNIT: Q
NESM SUBUNIT: R
NUPM SUBUNIT: S
NB6M SUBUNIT: T
NUXM SUBUNIT: U
NUYM SUBUNIT: V
NUZM SUBUNIT: W
NIAM SUBUNIT: X
NEBM SUBUNIT: Y
NB2M SUBUNIT: Z
NIDM SUBUNIT: 0
NUUM SUBUNIT: 1
NI8M SUBUNIT: 2
NI9M SUBUNIT: 3
N7BM SUBUNIT: 4
UNKNOWN SUBUNIT: 5
NB5M SUBUNIT: 6
NUNM SUBUNIT: 7
ND1 SUBUNIT (NU1M): 8
ND2 SUBUNIT (NU2M): 9
ND3 SUBUNIT (NU3M): a
ND4 SUBUNIT (NU4M): b
ND5 SUBUNIT (NU5M): c
ND6 SUBUNIT (NU6M): d
NB8M SUBUNIT: e
NIPM SUBUNIT: f

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
Y

W
Z

X
a

Y
b

Z
c

0
d

1
e

2
f

3
g

4
h

5
i

6
j

7
n

8
1

9
2

a
3

b
4

c
5

d
6

e
8

f
9

Membrane

We predict this structure to be a membrane protein.
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75-KDA PROTEIN (NUAM)

51-KDA PROTEIN (NUBM)

49-KDA PROTEIN (NUCM)

NIMM SUBUNIT

NUEM SUBUNIT

NUFM SUBUNIT

30-KDA PROTEIN (NUGM)

24-KDA SUBUNIT (NUHM)

TYKY SUBUNIT (NUIM)

NUJM SUBUNIT

PSST SUBUNIT (NUKM)

ND4L SUBUNIT (NULM)

NUMM SUBUNIT

ACPM1 SUBUNIT

NB4M SUBUNIT

ACPM2 SUBUNIT

NI2M SUBUNIT

NESM SUBUNIT

NUPM SUBUNIT

NB6M SUBUNIT

NUXM SUBUNIT

NUYM SUBUNIT

NUZM SUBUNIT

NIAM SUBUNIT

NEBM SUBUNIT

NB2M SUBUNIT

NIDM SUBUNIT

NUUM SUBUNIT

NI8M SUBUNIT

NI9M SUBUNIT

N7BM SUBUNIT

UNKNOWN SUBUNIT

NB5M SUBUNIT

NUNM SUBUNIT

ND1 SUBUNIT (NU1M)

ND2 SUBUNIT (NU2M)

ND3 SUBUNIT (NU3M)

ND4 SUBUNIT (NU4M)

ND5 SUBUNIT (NU5M)

ND6 SUBUNIT (NU6M)

NB8M SUBUNIT

NIPM SUBUNIT

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