8BQ5 image
Deposition Date 2022-11-18
Release Date 2023-03-22
Last Version Date 2024-10-09
Entry Detail
PDB ID:
8BQ5
Keywords:
MEMBRANE PROTEIN
Title:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 1 composition)
Biological Source:
Source Organism:
Arabidopsis thaliana (Taxon ID: 3702)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.73 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8BQ5 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 3
Gene (Uniprot):ND3
Chain IDs:A
Chain Length:65
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:P92533 Pfam ID:PF00507
Protein Blast
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
UniProt ID:Q9ZU25 Pfam ID:PF00675, PF05193
Protein Blast
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
UniProt ID:Q42290 Pfam ID:PF00675, PF05193
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b
Chain IDs:XA (auth: AC), HB (auth: BC)
Chain Length:393
Number of Molecules:2
Biological Source:Arabidopsis thaliana
UniProt ID:P42792 Pfam ID:PF00033, PF00032
Protein Blast
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
UniProt ID:Q94JS0 Pfam ID:PF02921, PF00355
Protein Blast
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
UniProt ID:Q9FKS5 Pfam ID:PF02167
Protein Blast
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
UniProt ID:F4JWS8 Pfam ID:PF02271
Protein Blast
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
UniProt ID:Q9SG91 Pfam ID:PF10890
Protein Blast
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
UniProt ID:Q0WWE3 Pfam ID:PF02320
Protein Blast
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
UniProt ID:Q9LXJ2 Pfam ID:PF05365
Protein Blast
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
UniProt ID:Q94K78
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Gene (Uniprot):T22P22_160
Chain IDs:B
Chain Length:65
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q42577 Pfam ID:PF01058
Protein Blast
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
UniProt ID:Q95748 Pfam ID:PF00329
Protein Blast
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
UniProt ID:P93306 Pfam ID:PF00346
Protein Blast
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
UniProt ID:O22769 Pfam ID:PF01257
Protein Blast
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
UniProt ID:Q9FNN5 Pfam ID:PF01512, PF22461, PF10531, PF10589
Protein Blast
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
UniProt ID:Q9FGI6 Pfam ID:PF13510, PF10588, PF22117, PF22151, PF00384, PF09326
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 1
Chain IDs:H
Chain Length:325
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:P92558 Pfam ID:PF00146
Protein Blast
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
UniProt ID:Q42599 Pfam ID:PF12838
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 6
Chain IDs:J
Chain Length:69
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:P60497 Pfam ID:PF00499
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase subunit 4L
Chain IDs:K
Chain Length:100
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q04614 Pfam ID:PF00420
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 5
Chain IDs:L
Chain Length:125
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:P29388 Pfam ID:PF00662, PF00361, PF06455
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4
Chain IDs:M
Chain Length:495
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:P93313 Pfam ID:PF00361
Protein Blast
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
UniProt ID:O05000 Pfam ID:PF00361
Protein Blast
Polymer Type:polypeptide(L)
Molecule:AT3G07480.1
Chain IDs:O
Chain Length:103
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q9SRR8
Protein Blast
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
UniProt ID:Q9SK66 Pfam ID:PF01370
Protein Blast
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
UniProt ID:Q9FJW4 Pfam ID:PF04800
Protein Blast
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
UniProt ID:Q9M9M6 Pfam ID:PF10276
Protein Blast
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
UniProt ID:Q9FIJ2 Pfam ID:PF05047
Protein Blast
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
UniProt ID:P53665 Pfam ID:PF00550
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein 2, mitochondrial
Gene (Uniprot):MTACP2
Chain IDs:U
Chain Length:63
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:O80800 Pfam ID:PF00550
Protein Blast
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
UniProt ID:Q9FLX7 Pfam ID:PF04716
Protein Blast
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
UniProt ID:Q9LHI0
Protein Blast
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
UniProt ID:Q8LGE7 Pfam ID:PF06747
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Outer envelope pore protein 16-3, chloroplastic/mitochondrial
Gene (Uniprot):OEP163
Chain IDs:Y
Chain Length:159
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:O48528 Pfam ID:PF02466
Protein Blast
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
UniProt ID:Q8RWA7 Pfam ID:PF06212
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Gene (Uniprot):F17O14.8
Chain IDs:AA (auth: a)
Chain Length:65
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q9C9Z5 Pfam ID:PF15879
Protein Blast
Polymer Type:polypeptide(L)
Molecule:At2g46540/F11C10.23
Gene (Uniprot):F13A10.7, F13A10_7
Chain IDs:BA (auth: b)
Chain Length:65
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q9ZPY5
Protein Blast
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
UniProt ID:Q8VZT9
Protein Blast
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
UniProt ID:Q94AL6
Protein Blast
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
UniProt ID:Q9LZI6 Pfam ID:PF10200
Protein Blast
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
UniProt ID:Q84W12 Pfam ID:PF10785
Protein Blast
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
UniProt ID:Q9SLC8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:P1
Chain IDs:HA (auth: i)
Chain Length:98
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q9FYF8 Pfam ID:PF17250
Protein Blast
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
UniProt ID:Q8LDK3
Protein Blast
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
UniProt ID:O64725 Pfam ID:PF08122
Protein Blast
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:125
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q9FGK0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:B15 -- 1 beta subcomplex subunit 4
Chain IDs:LA (auth: m)
Chain Length:495
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q9SIQ8
Protein Blast
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
UniProt ID:Q945M1
Protein Blast
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
UniProt ID:Q9SKC9 Pfam ID:PF05676
Protein Blast
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
UniProt ID:Q94C12 Pfam ID:PF10249
Protein Blast
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
UniProt ID:Q9M9M9 Pfam ID:PF05071
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein At1g67785
Gene (Uniprot):At1g67785
Chain IDs:QA (auth: u)
Chain Length:63
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q8VZ65
Protein Blast
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
UniProt ID:Q9ZUX4
Protein Blast
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
UniProt ID:Q9SMN1 EC:4.2.1.1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Gamma carbonic anhydrase 2, mitochondrial
Gene (Uniprot):GAMMACA2
Chain IDs:TA (auth: y)
Chain Length:159
Number of Molecules:1
Biological Source:Arabidopsis thaliana
UniProt ID:Q9C6B3 Pfam ID:PF00132 EC:4.2.1.1
Protein Blast
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
UniProt ID:Q9FWR5 EC:4.2.1.1
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME A MET modified residue
Ligand Molecules
8Q1
COO
FE
FES
FMN
HEM
NDP
SF4
UQ5
UQ7
UQ9
ZN
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8BQ5