8BED

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialA [auth E]255Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for O22769 (Arabidopsis thaliana)
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UniProt GroupO22769
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialB [auth F]486Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q9FNN5 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrialC [auth G]748Arabidopsis thalianaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for Q9FGI6 (Arabidopsis thaliana)
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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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialE [auth Q]154Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FJW4 (Arabidopsis thaliana)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialF [auth R]110Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M9M6 (Arabidopsis thaliana)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2G [auth S]97Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FIJ2 (Arabidopsis thaliana)
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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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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
J [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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K [auth F],
M [auth G],
N [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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I [auth E],
L [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
O [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.3
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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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