8BEE

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution.

Klusch, N.Dreimann, M.Senkler, J.Rugen, N.Kuhlbrandt, W.Braun, H.P.

(2023) Nat Plants 9: 142-156

  • DOI: https://doi.org/10.1038/s41477-022-01308-6
  • Primary Citation of Related Structures:  
    8BED, 8BEE, 8BEF, 8BEH, 8BEL, 8BEP, 8BPX, 8BQ5, 8BQ6

  • PubMed Abstract: 

    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 2 with a co-purified ubiquinone in the Q O site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.


  • Organizational Affiliation

    Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany. Niklas.Klusch@biophys.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialA [auth B]218Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q42577 (Arabidopsis thaliana)
Explore Q42577 
Go to UniProtKB:  Q42577
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42577
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3B [auth C]190Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q95748 (Arabidopsis thaliana)
Explore Q95748 
Go to UniProtKB:  Q95748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95748
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 7C [auth D]394Arabidopsis thalianaMutation(s): 1 
EC: 7.1.1.2
UniProt
Find proteins for P93306 (Arabidopsis thaliana)
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UniProt GroupP93306
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrialD [auth I]222Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q42599 (Arabidopsis thaliana)
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UniProt GroupQ42599
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialE [auth P]402Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SK66 (Arabidopsis thaliana)
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UniProt GroupQ9SK66
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein 2, mitochondrialF [auth U]126Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for O80800 (Arabidopsis thaliana)
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UniProt GroupO80800
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrialG [auth V]169Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FLX7 (Arabidopsis thaliana)
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UniProt GroupQ9FLX7
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6H [auth W]133Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9LHI0 (Arabidopsis thaliana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-AI [auth Z]143Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8RWA7 (Arabidopsis thaliana)
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UniProt GroupQ8RWA7
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12J [auth q]159Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M9M9 (Arabidopsis thaliana)
Explore Q9M9M9 
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UniProt GroupQ9M9M9
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
N [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

Download Ideal Coordinates CCD File 
O [auth W]S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
K [auth B],
L [auth I],
M [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.3
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection
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