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Structure paper

TitleCryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Journal, issue, pagesNat Plants, Vol. 9, Issue 1, Page 142-156, Year 2023
Publish dateDec 30, 2022
AuthorsNiklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
PubMed AbstractProtein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...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 III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
External linksNat Plants / PubMed:36585502 / PubMed Central
MethodsEM (single particle)
Resolution2.03 - 2.8 Å
Structure data

15998

8bed

EMDB-15998, PDB-8bed:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral tip)
Method: EM (single particle) / Resolution: 2.03 Å

15999

8bee

EMDB-15999, PDB-8bee:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)
Method: EM (single particle) / Resolution: 2.04 Å

16000

8bef

EMDB-16000, PDB-8bef:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane core)
Method: EM (single particle) / Resolution: 2.13 Å

16003

8beh

EMDB-16003, PDB-8beh:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)
Method: EM (single particle) / Resolution: 2.29 Å

16007

8bel

EMDB-16007, PDB-8bel:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)
Method: EM (single particle) / Resolution: 2.25 Å

16008

8bep

EMDB-16008, PDB-8bep:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
Method: EM (single particle) / Resolution: 2.29 Å

EMDB-16153: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete consensus)
Method: EM (single particle) / Resolution: 2.09 Å

EMDB-16156: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Conformation 1 membrane arm)
Method: EM (single particle) / Resolution: 2.53 Å

EMDB-16166: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Conformation 2 consensus)
Method: EM (single particle) / Resolution: 2.79 Å

EMDB-16167: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Conformation 1 consensus)
Method: EM (single particle) / Resolution: 2.73 Å

16168

8bpx

EMDB-16168, PDB-8bpx:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition)
Method: EM (single particle) / Resolution: 2.09 Å

16171

8bq5

EMDB-16171, PDB-8bq5:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 1 composition)
Method: EM (single particle) / Resolution: 2.73 Å

16172

8bq6

EMDB-16172, PDB-8bq6:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 2 composition)
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

ChemComp-8Q1:
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM / Phosphatidylglycerol

ChemComp-UQ9:
Ubiquinone-9

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

ChemComp-FE:
Unknown entry / Iron

ChemComp-UQ5:
2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE

ChemComp-PC7:
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM / Phosphatidylcholine

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Phosphatidic acid

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

ChemComp-BCO:
Butyryl Coenzyme A

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

ChemComp-UQ7:
UBIQUINONE-7

ChemComp-COO:
CROTONYL COENZYME A

Source
  • arabidopsis thaliana (thale cress)
  • thale cress (thale cress)
  • Arabidopsis t (thale cress)
KeywordsMEMBRANE PROTEIN / Plant / Mitochondria / Comple. / Complex

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