6X89 image
Deposition Date 2020-06-01
Release Date 2020-09-02
Last Version Date 2024-10-09
Entry Detail
PDB ID:
6X89
Title:
Vigna radiata mitochondrial complex I*
Biological Source:
Source Organism:
Vigna radiata (Taxon ID: 157791)
Method Details:
Experimental Method:
Resolution:
3.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NU1M
Chain IDs:Q (auth: 1M)
Chain Length:325
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:NU2M
Chain IDs:R (auth: 2M)
Chain Length:488
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:NU3M
Chain IDs:S (auth: 3M)
Chain Length:118
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:NU4L
Chain IDs:T (auth: 4L)
Chain Length:100
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:NU6M
Chain IDs:U (auth: 6M)
Chain Length:205
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:Unknown Peptide
Chain IDs:A
Chain Length:18
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Gene (Uniprot):LOC106758834
Chain IDs:V (auth: A1)
Chain Length:65
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Gene (Uniprot):LOC106759195
Chain IDs:B (auth: A2)
Chain Length:98
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uncharacterized protein LOC106754061
Gene (Uniprot):LOC106754061
Chain IDs:W (auth: A3)
Chain Length:63
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
Gene (Uniprot):LOC106760411
Chain IDs:C (auth: A5)
Chain Length:169
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Gene (Uniprot):LOC106780789
Chain IDs:D (auth: A6)
Chain Length:132
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NDUA7
Gene (Uniprot):LOC106768957
Chain IDs:E (auth: A7)
Chain Length:127
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
Gene (Uniprot):LOC106778955
Chain IDs:X (auth: A8)
Chain Length:106
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1
Gene (Uniprot):LOC106772694
Chain IDs:F (auth: A9)
Chain Length:396
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Gene (Uniprot):LOC106776991
Chain IDs:G (auth: AL)
Chain Length:156
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
Gene (Uniprot):LOC106769964
Chain IDs:Y (auth: AM)
Chain Length:143
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:Unknown Peptide
Chain IDs:Z (auth: B)
Chain Length:25
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:Unknown Peptide
Chain IDs:AA (auth: C)
Chain Length:43
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NDUC2
Gene (Uniprot):LOC106767534
Chain IDs:BA (auth: C2)
Chain Length:81
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gamma carbonic anhydrase 1, mitochondrial
Gene (Uniprot):LOC106778103
Chain IDs:FA (auth: G1)
Chain Length:270
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gamma carbonic anhydrase 1, mitochondrial-like
Gene (Uniprot):LOC106761993
Chain IDs:GA (auth: G2)
Chain Length:273
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gamma carbonic anhydrase-like 2, mitochondrial
Gene (Uniprot):LOC106765552
Chain IDs:HA (auth: L2)
Chain Length:256
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein At2g27730, mitochondrial
Gene (Uniprot):LOC106755236
Chain IDs:CA (auth: P2)
Chain Length:115
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
Gene (Uniprot):LOC106757688
Chain IDs:H (auth: S1)
Chain Length:746
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:NDUS2
Chain IDs:I (auth: S2)
Chain Length:394
Number of Molecules:1
Biological Source:Vigna radiata
Polymer Type:polypeptide(L)
Molecule:NDUS3
Chain IDs:J (auth: S3)
Chain Length:190
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Gene (Uniprot):LOC106765762
Chain IDs:K (auth: S4)
Chain Length:146
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:serine/arginine-rich-splicing factor SR34 isoform X2
Gene (Uniprot):LOC106757655
Chain IDs:DA (auth: S5)
Chain Length:399
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Gene (Uniprot):LOC106779709
Chain IDs:L (auth: S6)
Chain Length:103
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Gene (Uniprot):LOC106762764
Chain IDs:M (auth: S7)
Chain Length:213
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
Gene (Uniprot):LOC106775047
Chain IDs:N (auth: S8)
Chain Length:222
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Gene (Uniprot):LOC106772405
Chain IDs:O (auth: V1)
Chain Length:491
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Gene (Uniprot):LOC106762461
Chain IDs:P (auth: V2)
Chain Length:251
Number of Molecules:1
Biological Source:Vigna radiata
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NDUX1
Gene (Uniprot):LOC106775330
Chain IDs:EA (auth: X1)
Chain Length:101
Number of Molecules:1
Biological Source:Vigna radiata
Primary Citation
Atomic structure of a mitochondrial complex I intermediate from vascular plants.
Elife 9 ? ? (2020)
PMID: 32840211 DOI: 10.7554/eLife.56664

Abstact

Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large membrane-protein complexes. Complex I (CI) is the main entry point for electrons into the mETC. For plants, limited availability of mitochondrial material has curbed detailed biochemical and structural studies of their mETC. Here, we present the cryoEM structure of the known CI assembly intermediate CI* from Vigna radiata at 3.9 Å resolution. CI* contains CI's NADH-binding and CoQ-binding modules, the proximal-pumping module and the plant-specific γ-carbonic-anhydrase domain (γCA). Our structure reveals significant differences in core and accessory subunits of the plant complex compared to yeast, mammals and bacteria, as well as the details of the γCA domain subunit composition and membrane anchoring. The structure sheds light on differences in CI assembly across lineages and suggests potential physiological roles for CI* beyond assembly.

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