7QSD image
Deposition Date 2022-01-13
Release Date 2022-03-02
Last Version Date 2023-03-08
Entry Detail
PDB ID:
7QSD
Keywords:
OXIDOREDUCTASE
Title:
Bovine complex I in the active state at 3.1 A
Biological Source:
Source Organism:
Bos taurus (Taxon ID: 9913)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7QSD validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 3
Chain IDs:A
Chain Length:115
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P03898 Pfam ID:PF00507
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Gene (Uniprot):NDUFS7
Chain IDs:B
Chain Length:84
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P42026 Pfam ID:PF01058
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Gene (Uniprot):NDUFS3
Chain IDs:C
Chain Length:266
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P23709 Pfam ID:PF00329
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
Gene (Uniprot):NDUFS2
Mutations:Q129R (Q162R)
Chain IDs:D
Chain Length:120
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P17694 Pfam ID:PF00346 EC:7.1.1.2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Gene (Uniprot):NDUFV2
Chain IDs:E
Chain Length:249
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P04394 Pfam ID:PF01257
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Gene (Uniprot):NDUFV1
Chain IDs:F
Chain Length:57
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P25708 Pfam ID:PF01512, PF22461, PF10589
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
Gene (Uniprot):NDUFS1
Chain IDs:G
Chain Length:154
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P15690 Pfam ID:PF00111, PF10588, PF22117, PF22151, PF00384, PF09326
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 1
Gene (Uniprot):MT-ND1
Chain IDs:H
Chain Length:189
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P03887 Pfam ID:PF00146
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
Gene (Uniprot):NDUFS8
Chain IDs:I
Chain Length:127
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P42028 Pfam ID:PF12838
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 6
Gene (Uniprot):MT-ND6
Chain IDs:J
Chain Length:175
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P03924 Pfam ID:PF00499
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4L
Gene (Uniprot):MT-ND4L
Chain IDs:K
Chain Length:98
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P03902 Pfam ID:PF00420
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 5
Gene (Uniprot):MT-ND5
Chain IDs:L
Chain Length:606
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P03920 Pfam ID:PF00662, PF00361, PF06455
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4
Gene (Uniprot):MT-ND4
Chain IDs:M
Chain Length:129
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P03910 Pfam ID:PF01059, PF00361
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 2
Gene (Uniprot):MT-ND2
Chain IDs:N
Chain Length:347
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P03892 Pfam ID:PF00361, PF06444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Gene (Uniprot):NDUFA10
Mutations:N255K (N278K)
Chain IDs:O
Chain Length:343
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P34942 Pfam ID:PF01712
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Gene (Uniprot):NDUFA9
Chain IDs:P
Chain Length:176
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P34943 Pfam ID:PF01370
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Gene (Uniprot):NDUFS4
Chain IDs:Q
Chain Length:175
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02375 Pfam ID:PF04800
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Gene (Uniprot):NDUFS6
Chain IDs:R
Chain Length:124
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P23934 Pfam ID:PF10276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Gene (Uniprot):NDUFA2
Chain IDs:S
Chain Length:99
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02370 Pfam ID:PF05047
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitochondrial
Gene (Uniprot):NDUFAB1
Chain IDs:T, U
Chain Length:156
Number of Molecules:2
Biological Source:Bos taurus
UniProt ID:P52505 Pfam ID:PF00550
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Gene (Uniprot):NDUFA5
Chain IDs:V
Chain Length:116
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P23935 Pfam ID:PF04716
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Gene (Uniprot):NDUFA6
Chain IDs:W
Chain Length:128
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02366 Pfam ID:PF13233
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Gene (Uniprot):NDUFA8
Chain IDs:X
Chain Length:172
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P42029 Pfam ID:PF06747
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Gene (Uniprot):NDUFA11
Chain IDs:Y
Chain Length:141
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q8HXG6 Pfam ID:PF02466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Gene (Uniprot):NDUFA13
Chain IDs:Z
Chain Length:144
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q95KV7 Pfam ID:PF06212
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Gene (Uniprot):NDUFA1
Chain IDs:AA (auth: a)
Chain Length:115
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02377 Pfam ID:PF15879
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Gene (Uniprot):NDUFA3
Chain IDs:BA (auth: b)
Chain Length:84
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02371 Pfam ID:PF14987
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Gene (Uniprot):NDUFC1
Chain IDs:CA (auth: c)
Chain Length:266
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02376 Pfam ID:PF15088
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 subunit C2
Gene (Uniprot):NDUFC2
Chain IDs:DA (auth: d)
Chain Length:120
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02827 Pfam ID:PF06374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
Gene (Uniprot):NDUFS5
Chain IDs:EA (auth: e)
Chain Length:249
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02379 Pfam ID:PF10200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
Gene (Uniprot):NDUFB1
Chain IDs:FA (auth: f)
Chain Length:57
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02378 Pfam ID:PF08040
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
Gene (Uniprot):NDUFB11
Chain IDs:GA (auth: g)
Chain Length:154
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q8HXG5 Pfam ID:PF10183
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Gene (Uniprot):NDUFB5
Chain IDs:HA (auth: h)
Chain Length:189
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02380 Pfam ID:PF09781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Gene (Uniprot):NDUFB6
Chain IDs:IA (auth: i)
Chain Length:127
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02367 Pfam ID:PF09782
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Gene (Uniprot):NDUFB2
Chain IDs:JA (auth: j)
Chain Length:175
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02374 Pfam ID:PF14813
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
Gene (Uniprot):NDUFB3
Chain IDs:KA (auth: k)
Chain Length:98
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02365 Pfam ID:PF08122
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Gene (Uniprot):NDUFB8
Chain IDs:LA (auth: l)
Chain Length:606
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02372 Pfam ID:PF05821
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Gene (Uniprot):NDUFB4
Chain IDs:MA (auth: m)
Chain Length:129
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P48305 Pfam ID:PF07225
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Gene (Uniprot):NDUFB9
Chain IDs:NA (auth: n)
Chain Length:347
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02369 Pfam ID:PF05347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
Gene (Uniprot):NDUFB7
Chain IDs:OA (auth: o)
Chain Length:343
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02368 Pfam ID:PF05676
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Gene (Uniprot):NDUFB10
Chain IDs:PA (auth: p)
Chain Length:176
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q02373 Pfam ID:PF10249
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Gene (Uniprot):NDUFA12
Chain IDs:QA (auth: q)
Chain Length:175
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:O97725 Pfam ID:PF05071
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Gene (Uniprot):NDUFA7
Chain IDs:RA (auth: r)
Chain Length:124
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:Q05752 Pfam ID:PF07347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
Gene (Uniprot):NDUFV3
Chain IDs:SA (auth: s)
Chain Length:99
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P25712 Pfam ID:PF15880
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MR D ARG modified residue
AME DA MET modified residue
AYA Y ALA modified residue
FME A MET modified residue
SAC IA SER modified residue
Ligand Molecules
3PE
CDL
EHZ
FES
FMN
GTP
LMT
MG
NDP
PC1
SF4
ZN
Primary Citation
Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides.
Science 379 351 357 (2023)
PMID: 36701435 DOI: 10.1126/science.ade3332

Abstact

The molecular mode of action of biguanides, including the drug metformin, which is widely used in the treatment of diabetes, is incompletely characterized. Here, we define the inhibitory drug-target interaction(s) of a model biguanide with mammalian respiratory complex I by combining cryo-electron microscopy and enzyme kinetics. We interpret these data to explain the selectivity of biguanide binding to different enzyme states. The primary inhibitory site is in an amphipathic region of the quinone-binding channel, and an additional binding site is in a pocket on the intermembrane-space side of the enzyme. An independent local chaotropic interaction, not previously described for any drug, displaces a portion of a key helix in the membrane domain. Our data provide a structural basis for biguanide action and enable the rational design of medicinal biguanides.

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Protein

Chemical

Disease

Primary Citation of related structures
7QSD