7A24

Assembly intermediate of the plant mitochondrial complex I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM.

Soufari, H.Parrot, C.Kuhn, L.Waltz, F.Hashem, Y.

(2020) Nat Commun 11: 5195-5195

  • DOI: 10.1038/s41467-020-18814-w
  • Primary Citation of Related Structures:  
    7A23, 7A24

  • PubMed Abstract: 
  • Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes ...

    Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole P D module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the P P to the P D module.


    Organizational Affiliation

    Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, F-33600, Pessac, France. yaser.hashem@inserm.fr.



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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
51kDaA486Brassica oleraceaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 2
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Nad2mB [auth I]499Brassica oleraceaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Nad3mC [auth J]119Brassica oleraceaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Nad6mD [auth N]205Brassica oleraceaMutation(s): 0 
EC: 7.1.1.2
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Nad1mE [auth H]325Brassica oleraceaMutation(s): 0 
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Nad4LmF [auth K]100Brassica oleraceaMutation(s): 0 
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PGIVG [auth Y]106Brassica oleraceaMutation(s): 0 
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MWFEI [auth V]65Brassica oleraceaMutation(s): 0 
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B14.5aK [auth S]131Brassica oleraceaMutation(s): 0 
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75kDaO [auth C]748Brassica oleraceaMutation(s): 0 
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39kDaP [auth T]402Brassica oleraceaMutation(s): 0 
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Nad9mQ [auth F]190Brassica oleraceaMutation(s): 0 
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24kDaR [auth B]255Brassica oleraceaMutation(s): 0 
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13kDaT [auth P]110Brassica oleraceaMutation(s): 0 
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PSSTW [auth E]218Brassica oleraceaMutation(s): 0 
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TYKYX [auth D]222Brassica oleraceaMutation(s): 0 
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B14Y [auth X]133Brassica oleraceaMutation(s): 0 
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MNLLZ [auth c]106Brassica oleraceaMutation(s): 0 
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B8AA [auth Q]97Brassica oleraceaMutation(s): 0 
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ACPM1BA [auth k]122Brassica oleraceaMutation(s): 0 
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Unk1CA [auth r]24Brassica oleraceaMutation(s): 0 
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P2DA [auth n]113Brassica oleraceaMutation(s): 0 
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CAL1EA [auth o]252Brassica oleraceaMutation(s): 0 
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CA1GA [auth p], FA [auth q]275Brassica oleraceaMutation(s): 0 
EC: 4.2.1
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Entity ID: 33
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GLDHHA [auth z]610Brassica oleraceaMutation(s): 0 
EC: 1.3.2.3
Membrane Entity: Yes 
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Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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LA [auth i]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
T7X (Subject of Investigation/LOI)
Query on T7X

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KA [auth I], WA [auth c]Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
 Ligand Interaction
NDP (Subject of Investigation/LOI)
Query on NDP

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QA [auth T]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
PEV (Subject of Investigation/LOI)
Query on PEV

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MA [auth G](1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

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JA [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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IA [auth A], NA [auth C], OA [auth C], TA [auth E], UA [auth D], VA [auth D]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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PA [auth C], RA [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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SA [auth P], XA [auth q]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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YA [auth q]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-16-CE11-0024-02
European Research Council (ERC)759120

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release