SMTL ID : 6x89.1

Vigna radiata mitochondrial complex I*

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 21 residues within 4Å: Chain F: G.69, T.71, G.72, F.73, L.74, R.94, L.138, I.139, G.140, R.141, Y.148, M.157, V.177, S.178, C.179, K.194, P.213, A.214, V.215, R.222 Chain M: K.213 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain M Hydrogen bonds: F:G.69, F:T.71, F:F.73, F:L.74, F:R.94, F:L.138, F:Y.148, F:K.194 Salt bridges: F:R.94, F:R.141, F:R.222, F:R.222, M:K.213 pi-Cation interactions: F:R.94, F:R.94

6 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 7 residues within 4Å: Chain G: R.31, P.34 Chain M: K.66, L.70, W.73, R.76 Chain Q: L.49 6 PLIP interactions: 4 interactions with chain M, 2 interactions with chain G Hydrophobic interactions: M:K.66, M:L.70, M:L.70, G:P.34 Salt bridges: M:R.76, G:R.31 PC1.6: 18 residues within 4Å: Chain I: R.197, Q.201 Chain N: T.70, L.71, F.72, L.73 Chain Q: P.185, V.188, M.189, I.192, V.283, Y.290, L.298, V.302, L.306, W.310 Chain W: F.26 Chain Y: F.57 13 PLIP interactions: 3 interactions with chain N, 7 interactions with chain Q, 1 interactions with chain Y, 1 interactions with chain I, 1 interactions with chain W Hydrophobic interactions: N:L.71, N:F.72, N:F.72, Q:P.185, Q:P.185, Q:V.188, Q:I.192, Q:V.283, Q:L.306, Q:W.310, Y:F.57, W:F.26 Salt bridges: I:R.197 PC1.14: 8 residues within 4Å: Chain G: L.39, I.43 Chain Q: S.45, F.46 Chain V: N.2, L.3, R.4, M.6 5 PLIP interactions: 3 interactions with chain V, 1 interactions with chain Q, 1 interactions with chain G Hydrophobic interactions: V:M.6, Q:F.46, G:L.39 Salt bridges: V:R.4, V:R.4 PC1.15: 10 residues within 4Å: Chain 1: H.31, W.33, E.34, V.37 Chain 5: R.24, L.25, R.28 Chain 7: Y.238 Ligands: PC1.16, PC1.17 5 PLIP interactions: 4 interactions with chain 1, 1 interactions with chain 5 Hydrophobic interactions: 1:W.33, 1:E.34, 1:V.37, 5:L.25 Salt bridges: 1:H.31 PC1.16: 11 residues within 4Å: Chain 2: R.85, A.88, V.89 Chain 4: Y.49, L.50, I.53 Chain 5: L.25, R.28, Y.33 Ligands: PC1.15, PC1.17 2 PLIP interactions: 1 interactions with chain 5, 1 interactions with chain 4 Hydrophobic interactions: 5:L.25 Hydrogen bonds: 4:Y.49 PC1.17: 8 residues within 4Å: Chain 4: L.50, K.54 Chain 5: Q.36 Chain 6: K.229, K.233 Chain R: W.45 Ligands: PC1.15, PC1.16 5 PLIP interactions: 2 interactions with chain R, 2 interactions with chain 4, 1 interactions with chain 6 Hydrophobic interactions: R:W.45, R:W.45, 4:L.50, 4:K.54 Salt bridges: 6:K.233

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

SF4.3: 11 residues within 4Å: Chain H: H.167, D.170, C.171, C.174, G.177, C.180, L.182, Q.183, V.271, G.272 Chain I: I.310 5 PLIP interactions: 5 interactions with chain H, Salt bridges: H:D.170 Metal complexes: H:H.167, H:C.171, H:C.174, H:C.180 SF4.4: 11 residues within 4Å: Chain H: R.218, C.219, I.220, Q.221, C.222, C.225, I.249, C.269, P.270, V.271, A.273 3 PLIP interactions: 3 interactions with chain H, Metal complexes: H:C.219, H:C.222, H:C.269 SF4.8: 11 residues within 4Å: Chain I: R.69 Chain M: A.87, C.88, C.89, G.124, T.125, G.151, S.152, C.153, Y.160, C.183 1 PLIP interactions: 1 interactions with chain I, pi-Cation interactions: I:H.154 SF4.9: 11 residues within 4Å: Chain N: H.111, C.133, P.134, I.138, C.162, I.163, C.165, G.166, F.167, C.168, E.179 5 PLIP interactions: 5 interactions with chain N, Salt bridges: N:E.179 Metal complexes: N:C.133, N:C.162, N:C.165, N:C.168 SF4.10: 14 residues within 4Å: Chain N: C.123, I.124, A.125, C.126, K.127, L.128, C.129, I.140, Y.155, C.172, P.173, V.174, A.176, I.177 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.123, N:C.126, N:C.129, N:C.172 SF4.11: 12 residues within 4Å: Chain O: I.233, P.251, S.406, C.407, G.408, Q.409, C.410, C.413, T.451, I.452, C.453, L.455 1 PLIP interactions: 1 interactions with chain O, Metal complexes: O:C.413

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

FES.5: 9 residues within 4Å: Chain H: R.105, C.107, Y.108, G.116, N.117, C.118, R.119, C.121, C.135 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.107, H:C.118, H:C.121, H:C.135 FES.13: 6 residues within 4Å: Chain P: C.126, T.128, C.131, C.167, G.169, C.171 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.126, P:C.131, P:C.167, P:C.171

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain L: C.65, H.75, C.90, Y.92, C.93 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.65, L:H.75, L:C.90, L:Y.92, L:C.93 ZN.18: 5 residues within 4Å: Chain 5: Q.101, H.130, Y.207 Chain 6: H.107, H.135 3 PLIP interactions: 2 interactions with chain 6, 1 interactions with chain 5 Metal complexes: 6:H.107, 6:H.135, 5:H.130

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.12: 18 residues within 4Å: Chain O: G.115, R.116, G.117, A.119, K.126, N.144, D.146, E.147, S.148, Y.232, G.235, E.236, E.237, V.270, T.271, N.272, A.454, L.455 14 PLIP interactions: 14 interactions with chain O Hydrophobic interactions: O:Y.232, O:Y.232, O:E.236, O:E.236, O:A.454, O:L.455 Hydrogen bonds: O:G.117, O:N.144, O:N.144, O:S.148, O:E.237, O:E.237, O:N.272, O:N.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maldonado, M. et al., Atomic structure of a mitochondrial complex I intermediate from vascular plants. Elife (2020)

Release Date

2020-09-02

Peptides

Unknown Peptide: A
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: B
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: D
NDUA7: E
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1: F
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: G
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial: H
NDUS2: I
NDUS3: J
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: K
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: L
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: M
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: N
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: O
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: P
NU1M: Q
NU2M: R
NU3M: S
NU4L: T
NU6M: U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: V
uncharacterized protein LOC106754061: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A: Y
Unknown Peptide: Z
Unknown Peptide: 0
NDUC2: 1
Protein At2g27730, mitochondrial: 2
serine/arginine-rich-splicing factor SR34 isoform X2: 3
NDUX1: 4
gamma carbonic anhydrase 1, mitochondrial: 5
gamma carbonic anhydrase 1, mitochondrial-like: 6
gamma carbonic anhydrase-like 2, mitochondrial: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A2

C
A5

D
A6

E
A7

F
A9

G
AL

H
S1

I
S2

J
S3

K
S4

L
S6

M
S7

N
S8

O
V1

P
V2

Q
1M

R
2M

S
3M

T
4L

U
6M

V
A1

W
A3

X
A8

Y
AM

Z
B

0
C

1
C2

2
P2

3
S5

4
X1

5
G1

6
G2

7
L2

Membrane

We predict this structure to be a membrane protein.
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Unknown Peptide

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NDUA7

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial

NDUS2

NDUS3

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

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

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

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

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NU1M

NU2M

NU3M

NU4L

NU6M

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

uncharacterized protein LOC106754061

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A

Unknown Peptide

Unknown Peptide

NDUC2

Protein At2g27730, mitochondrial

serine/arginine-rich-splicing factor SR34 isoform X2

NDUX1

gamma carbonic anhydrase 1, mitochondrial

gamma carbonic anhydrase 1, mitochondrial-like

gamma carbonic anhydrase-like 2, mitochondrial

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