ISDA

Deposition Date 2022-02-08

Release Date 2023-02-08

Last Version Date 2023-02-08

Entry Detail

PDB ID:

7R4D

Keywords:

OXIDOREDUCTASE

Title:

Bovine complex I in the presence of IM1761092, deactive class vi (Composite map)

Biological Source:

Source Organism:

Bos taurus (Taxon ID: 9913)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.30 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 3
Chain IDs:A
Chain Length:70
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:Q166R
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:727
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:212
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:108
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:186
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:179
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:N278K
Chain IDs:O
Chain Length:137
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:70
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:727
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:212
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:108
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:186
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:179
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:137
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
2MR	D	ARG	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

I49

LMT

MYR

NDP

PC1

SF4

Primary Citation

Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides.

Bridges, H.R, Blaza, J.N, Yin, Z, Chung, I, Pollak, M.N, Hirst, J.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures