8BPX image
Deposition Date 2022-11-18
Release Date 2023-01-25
Last Version Date 2024-11-06
Entry Detail
PDB ID:
8BPX
Title:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.09 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 3
Gene (Uniprot):ND3
Chain IDs:A
Chain Length:119
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
Gene (Uniprot):MPPalpha1
Chain IDs:VA (auth: AA), FB (auth: BA)
Chain Length:503
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Probable mitochondrial-processing peptidase subunit beta, mitochondrial
Gene (Uniprot):MPPbeta
Chain IDs:WA (auth: AB), GB (auth: BB)
Chain Length:531
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b
Gene (Uniprot):MT-CYB, At2g07727
Chain IDs:XA (auth: AC), HB (auth: BC)
Chain Length:393
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
Gene (Uniprot):UCR1-1
Chain IDs:YA (auth: AD), IB (auth: BD)
Chain Length:272
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome c1 2, heme protein, mitochondrial
Gene (Uniprot):CYC1-2
Chain IDs:ZA (auth: AE), JB (auth: BE)
Chain Length:307
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 7-2, mitochondrial
Gene (Uniprot):QCR7-2
Chain IDs:AB (auth: AF), KB (auth: BF)
Chain Length:122
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 8-1, mitochondrial
Gene (Uniprot):UCRQ-1
Chain IDs:BB (auth: AG), LB (auth: BG)
Chain Length:72
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 6-1, mitochondrial
Gene (Uniprot):QCR6-1
Chain IDs:CB (auth: AH), MB (auth: BH)
Chain Length:69
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 9, mitochondrial
Gene (Uniprot):QCR9
Chain IDs:DB (auth: AI), NB (auth: BI)
Chain Length:72
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 10, mitochondrial
Gene (Uniprot):UCRY
Chain IDs:EB (auth: AJ), OB (auth: BJ)
Chain Length:57
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Gene (Uniprot):T22P22_160
Chain IDs:B
Chain Length:218
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
Gene (Uniprot):NAD9
Chain IDs:C
Chain Length:88
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
Gene (Uniprot):NAD7
Chain IDs:D
Chain Length:81
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Gene (Uniprot):T10P11.14
Chain IDs:E
Chain Length:83
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Gene (Uniprot):MAH20.9
Chain IDs:F
Chain Length:486
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
Gene (Uniprot):EMB1467
Chain IDs:G
Chain Length:748
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 1
Gene (Uniprot):ND1, At2g07785, At2g07786
Chain IDs:H
Chain Length:325
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
Gene (Uniprot):YUP8H12R.37, YUP8H12R_21
Chain IDs:I
Chain Length:98
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 6
Gene (Uniprot):ND6
Chain IDs:J
Chain Length:69
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4L
Gene (Uniprot):ND4L
Chain IDs:K
Chain Length:100
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 5
Gene (Uniprot):ND5
Chain IDs:L
Chain Length:669
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4
Gene (Uniprot):ND4
Chain IDs:M
Chain Length:495
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 2
Gene (Uniprot):ND2
Chain IDs:N
Chain Length:117
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:2Fe-2S ferredoxin-like superfamily protein
Gene (Uniprot):F21O3.19
Chain IDs:O
Chain Length:103
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Gene (Uniprot):F11A3.9
Chain IDs:P
Chain Length:106
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Gene (Uniprot):FRO1
Chain IDs:Q
Chain Length:159
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Gene (Uniprot):T17B22_24
Chain IDs:R
Chain Length:110
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Gene (Uniprot):MCA23_23
Chain IDs:S
Chain Length:97
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein 1, mitochondrial
Gene (Uniprot):MTACP1
Chain IDs:T
Chain Length:122
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein 2, mitochondrial
Gene (Uniprot):MTACP2
Chain IDs:U
Chain Length:126
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
Gene (Uniprot):MXC20.6
Chain IDs:V
Chain Length:169
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Gene (Uniprot):F28J15.12, MQC3.9
Chain IDs:W
Chain Length:133
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
Gene (Uniprot):F17K4.50
Chain IDs:X
Chain Length:256
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Outer envelope pore protein 16-3, chloroplastic/mitochondrial
Gene (Uniprot):OEP163
Chain IDs:Y
Chain Length:278
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
Gene (Uniprot):MEE4
Chain IDs:Z
Chain Length:275
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Gene (Uniprot):F17O14.8
Chain IDs:AA (auth: a)
Chain Length:119
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:At2g46540/F11C10.23
Gene (Uniprot):F13A10.7, F13A10_7
Chain IDs:BA (auth: b)
Chain Length:218
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein
Gene (Uniprot):At4g00585
Chain IDs:CA (auth: c)
Chain Length:88
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Excitatory amino acid transporter
Gene (Uniprot):F1C12.70, F1C12_70
Chain IDs:DA (auth: d)
Chain Length:81
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
Gene (Uniprot):F26K9_220
Chain IDs:EA (auth: e)
Chain Length:83
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:At4g16450
Gene (Uniprot):DL4250W
Chain IDs:FA (auth: f)
Chain Length:486
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
Gene (Uniprot):MHK10.3
Chain IDs:GA (auth: g)
Chain Length:748
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:At1g67350
Gene (Uniprot):F1N21.17
Chain IDs:HA (auth: i)
Chain Length:98
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
Gene (Uniprot):T23E18.30
Chain IDs:IA (auth: j)
Chain Length:69
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
Gene (Uniprot):T8K22.19
Chain IDs:JA (auth: k)
Chain Length:100
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Gene (Uniprot):MNJ7.16
Chain IDs:KA (auth: l)
Chain Length:669
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:AT2G31490 protein
Gene (Uniprot):T28P16.2, T28P16_2
Chain IDs:LA (auth: m)
Chain Length:495
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Gene (Uniprot):CIB22
Chain IDs:MA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
Gene (Uniprot):F14H20.12
Chain IDs:NA (auth: o)
Chain Length:103
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
Gene (Uniprot):MYF24_12
Chain IDs:OA (auth: p)
Chain Length:106
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Gene (Uniprot):T17B22.21
Chain IDs:PA (auth: q)
Chain Length:159
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein At1g67785
Gene (Uniprot):At1g67785
Chain IDs:QA (auth: u)
Chain Length:126
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein At2g27730, mitochondrial
Gene (Uniprot):F15K20.17
Chain IDs:RA (auth: v)
Chain Length:169
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Gamma carbonic anhydrase-like 2, mitochondrial
Gene (Uniprot):GAMMACAL2
Chain IDs:SA (auth: x)
Chain Length:256
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Gamma carbonic anhydrase 2, mitochondrial
Gene (Uniprot):GAMMACA2
Chain IDs:TA (auth: y)
Chain Length:278
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Gamma carbonic anhydrase 1, mitochondrial
Gene (Uniprot):GAMMACA1
Chain IDs:UA (auth: z)
Chain Length:275
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME A MET modified residue
Primary Citation
Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution.
Nat.Plants 9 142 156 (2023)
PMID: 36585502 DOI: 10.1038/s41477-022-01308-6

Abstact

Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III2 with a co-purified ubiquinone in the QO site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.

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Primary Citation of related structures