Brand  (β version)

PDB ID: 6RFQ

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Ligands
Code Name Style Show Link
3PE 1,2-distearoyl-sn-glycerophosphoethanolamine PoSSuM
CDL Cardiolipin PoSSuM
CPL 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine PoSSuM
FES Fe2/s2 (inorganic) cluster PoSSuM
FMN Flavin mononucleotide PoSSuM
LMN Lauryl maltose neopentyl glycol PoSSuM
NDP Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate PoSSuM
PLC Diundecyl phosphatidyl choline PoSSuM
SF4 Iron/sulfur cluster PoSSuM
T7X Phosphatidylinositol PoSSuM
ZMP S-[2-({N-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 6RFQ   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE
Title : Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2
Release Data : 2018-10-10
Compound :
mol_id molecule chains
1 Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I) A
ec: 1.6.99.3
mol_id molecule chains
2 Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I) B
ec: 1.6.99.3,7.1.1.2
mol_id molecule chains
3 Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I) C
ec: 1.6.99.3
mol_id molecule chains
4 Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I) D
mol_id molecule chains
5 Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I) E
mol_id molecule chains
6 Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I) F
mol_id molecule chains
7 Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I) G
ec: 1.6.99.3
mol_id molecule chains
8 Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I) H
ec: 1.6.99.3
mol_id molecule chains
9 Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I) I
ec: 1.6.99.3
mol_id molecule chains
10 Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I) J
mol_id molecule chains
11 Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I) K
ec: 1.6.99.3
mol_id molecule chains synonym
12 Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I) L NADH dehydrogenase subunit 4L, subunit ND4L
ec: 7.1.1.2
mol_id molecule chains
13 Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I) O
mol_id molecule chains
14 Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I) P
mol_id molecule chains
15 Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I) Q
mol_id molecule chains
16 Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I) R
mol_id molecule chains
17 Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I) S
ec: 1.6.99.3
mol_id molecule chains
18 Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I) U
mol_id molecule chains
19 Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I) W
mol_id molecule chains
20 Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I) X
mol_id molecule chains
21 Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I) Y
mol_id molecule chains
22 Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I) Z
mol_id molecule chains
23 Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I) a
mol_id molecule chains
24 Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I) b
mol_id molecule chains
25 Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I) c
mol_id molecule chains
26 Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I) d
mol_id molecule chains
27 Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I) e
mol_id molecule chains
28 Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I) f
mol_id molecule chains
29 Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I) g
mol_id molecule chains
30 Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I) i
mol_id molecule chains
31 Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I) j
ec: 1.6.99.3
mol_id molecule chains
32 Subunit N7BML assembly factor k
mol_id molecule chains
33 Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I) n
mol_id molecule chains
34 Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I) 1
ec: 7.1.1.2
mol_id molecule chains
35 Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I) 2
ec: 1.6.5.3
mol_id molecule chains
36 Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I) 3
ec: 7.1.1.2
mol_id molecule chains
37 Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I) 4
ec: 7.1.1.2
mol_id molecule chains
38 Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I) 5
ec: 7.1.1.2
mol_id molecule chains synonym
39 Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I) 6 NADH dehydrogenase subunit 6, Subunit ND6
ec: 7.1.1.2
mol_id molecule chains
40 Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I) 8
mol_id molecule chains
41 Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I) 9
Source :
mol_id organism_scientific organism_common
1 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
2 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
3 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
4 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
5 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
6 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
7 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
8 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
9 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
10 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
11 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
12 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
13 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
14 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
15 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
16 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
17 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
18 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
19 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
20 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
21 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
22 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
23 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
24 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
25 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
26 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
27 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
28 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
29 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
30 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
31 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific
32 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
33 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
34 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
35 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
36 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
37 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
38 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific
39 Yarrowia lipolytica  (taxid:4952)
mol_id organism_scientific organism_common
40 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
mol_id organism_scientific organism_common
41 Yarrowia lipolytica  (taxid:4952) Candida lipolytica
Authors : Parey, K., Vonck, J.
Keywords : Complex I, NADH dehydrogenase, Mitochondrion Proton pumping, Ubiquinone, OXIDOREDUCTASE
Exp. method : ELECTRON MICROSCOPY ( 3.3 Å )
Citation :

High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.

Parey, K.,Haapanen, O.,Sharma, V.  et al.
(2019)  Sci Adv  5 : eaax9484 - eaax9484

PubMed: 31844670
DOI: 10.1126/sciadv.aax9484

Reaction

Chain : A
UniProt : Q9UUU3 (Q9UUU3_YARLL)
Reaction : -
Cofactor: Evidence: Note:
[2Fe-2S] cluster ECO:0000256 | ARBA:ARBA00034078
-
[4Fe-4S] cluster ECO:0000256 | ARBA:ARBA00001966
-
Chain : B
UniProt : Q9UUU2 (Q9UUU2_YARLL)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 ARBA:ARBA00049551, RuleBase:RU364066
-
Cofactor: Evidence: Note:
FMN ECO:0000256 | ARBA:ARBA00001917
ECO:0000256 | RuleBase:RU364066
-
[4Fe-4S] cluster ECO:0000256 | ARBA:ARBA00001966
ECO:0000256 | RuleBase:RU364066
-
Chain : C
UniProt : Q9UUU1 (Q9UUU1_YARLL)
Reaction : -
Chain : D
UniProt : A0A1D8NC63 (A0A1D8NC63_YARLL)
Reaction : -
Chain : E
UniProt : A0A371BY45 (A0A371BY45_YARLL)
Reaction : -
Chain : F
UniProt : A0A371C5F3 (A0A371C5F3_YARLL)
Reaction : -
Chain : G
UniProt : Q9UUU0 (Q9UUU0_YARLL)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 ARBA:ARBA00049551
-
Chain : H
UniProt : Q9UUT9 (Q9UUT9_YARLL)
Reaction : -
Cofactor: Evidence: Note:
[2Fe-2S] cluster ECO:0000256 | ARBA:ARBA00034078
-
[2Fe-2S] cluster ECO:0000256 | PIRSR:PIRSR000216-1
Binds 1 [2Fe-2S] cluster.
Chain : I
UniProt : Q9UUT8 (Q9UUT8_YARLL)
Reaction : -
Cofactor: Evidence: Note:
[4Fe-4S] cluster ECO:0000256 | ARBA:ARBA00001966
-
Chain : J
UniProt : A0A371CB65 (A0A371CB65_YARLL)
Reaction : -
Chain : K
UniProt : Q9UUT7 (Q9UUT7_YARLL)
Reaction : -
Chain : L
UniProt : Q9B6D4 (NU4LM_YARLI)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 -
-
Chain : O
UniProt : A0A1H6PXT9 (A0A1H6PXT9_YARLL)
Reaction : -
Chain : P
UniProt : A0A1D8N3C8 (A0A1D8N3C8_YARLL)
Reaction : -
Chain : Q
UniProt : A0A1D8NG21 (A0A1D8NG21_YARLL)
Reaction : -
Chain : R
UniProt : A0A1D8NDL1 (A0A1D8NDL1_YARLL)
Reaction : -
Chain : S
UniProt : Q6ZY23 (Q6ZY23_YARLL)
Reaction : -
Chain : U
UniProt : A0A371C2D0 (A0A371C2D0_YARLL)
Reaction : -
Chain : W
UniProt : A0A1H6PPE5 (A0A1H6PPE5_YARLL)
Reaction : -
Chain : X
UniProt : A0A1D8NKB4 (A0A1D8NKB4_YARLL)
Reaction : -
Chain : Y
UniProt : A0A1D8N7X0 (A0A1D8N7X0_YARLL)
Reaction : -
Chain : Z
UniProt : A0A1D8N3H5 (A0A1D8N3H5_YARLL)
Reaction : -
Chain : a
UniProt : A0A1D8ND94 (A0A1D8ND94_YARLL)
Reaction : -
Chain : b
UniProt : A0A1D8NGI5 (A0A1D8NGI5_YARLL)
Reaction : -
Chain : c
UniProt : A0A371C0F2 (A0A371C0F2_YARLL)
Reaction : -
Chain : d
UniProt : A0A1D8N596 (A0A1D8N596_YARLL)
Reaction : -
Chain : e
UniProt : A0A1D8NFX6 (A0A1D8NFX6_YARLL)
Reaction : -
Chain : f
UniProt : A0A1H6PJS3 (A0A1H6PJS3_YARLL)
Reaction : -
Chain : g
UniProt : A0A1D8NJR0 (A0A1D8NJR0_YARLL)
Reaction : -
Chain : i
UniProt : A0A1H6Q311 (A0A1H6Q311_YARLL)
Reaction : -
Chain : j
UniProt : Q6ZY24 (Q6ZY24_YARLL)
Reaction : -
Chain : k
UniProt : A0A1D8NGE3 (A0A1D8NGE3_YARLL)
Reaction : -
Chain : n
UniProt : A0A371CFV9 (A0A371CFV9_YARLL)
Reaction : -
Chain : 1
UniProt : S5U3V2 (S5U3V2_YARLL)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 RuleBase:RU000473
-
Chain : 2
UniProt : S5U4R9 (S5U4R9_YARLL)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 ARBA:ARBA00049551
-
Chain : 3
UniProt : S5TMS4 (S5TMS4_YARLL)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 ARBA:ARBA00049551, RuleBase:RU003640
-
Chain : 4
UniProt : S5TMP9 (S5TMP9_YARLL)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 RuleBase:RU003297
-
Chain : 5
UniProt : S5TF58 (S5TF58_YARLL)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 RuleBase:RU003404
-
Chain : 6
UniProt : Q9B6E9 (NU6M_YARLI)
Reaction: EC: Evidence:
Physiological Direction:
a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) 7.1.1.2 -
-
Chain : 8
UniProt : A0A1H6PKH9 (A0A1H6PKH9_YARLL)
Reaction : -
Chain : 9
UniProt : A0A1D8NNZ0 (A0A1D8NNZ0_YARLL)
Reaction : -