7A23

Plant mitochondrial respiratory complex I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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: https://doi.org/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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
51kDa486Brassica oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nad2mB [auth I]499Brassica oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nad3mC [auth J]119Brassica oleraceaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nad6mD [auth N]205Brassica oleraceaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nad1mE [auth H]325Brassica oleraceaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nad4LmF [auth K]100Brassica oleraceaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PGIVG [auth Y]106Brassica oleraceaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
B16.6H [auth Z]143Brassica oleraceaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
MWFEI [auth V]65Brassica oleraceaMutation(s): 0 
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B9J [auth W]65Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
B14.5aK [auth S]131Brassica oleraceaMutation(s): 0 
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B14.5bL [auth i]81Brassica oleraceaMutation(s): 0 
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15kDaM [auth j]83Brassica oleraceaMutation(s): 0 
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Nad7mN [auth G]394Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
75kDaO [auth C]748Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
39kDaP [auth T]402Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Nad9mQ [auth F]190Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
24kDaR [auth B]255Brassica oleraceaMutation(s): 0 
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18kDaS [auth O]154Brassica oleraceaMutation(s): 0 
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13kDaT [auth P]110Brassica oleraceaMutation(s): 0 
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B13U [auth R]169Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
B17.2V [auth U]159Brassica oleraceaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
PSSTW [auth E]218Brassica oleraceaMutation(s): 0 
Membrane Entity: Yes 
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MoleculeChains Sequence LengthOrganismDetailsImage
TYKYX [auth D]222Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
B14Y [auth X]133Brassica oleraceaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
20.9kDaZ [auth c]106Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
B8AA [auth Q]97Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
ACPM1BA [auth k]122Brassica oleraceaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
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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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
CA1FA [auth q],
GA [auth p]
275Brassica oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Nad4mHA [auth M]495Brassica oleraceaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
PDSWIA [auth f]107Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
ESSSJA [auth g]114Brassica oleraceaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
B22KA [auth d]117Brassica oleraceaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Nad5mLA [auth a]669Brassica oleraceaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
B18MA [auth b]103Brassica oleraceaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
AGGGNA [auth h]69Brassica oleraceaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
ACPM2OA [auth e]126Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
B15PA [auth l]71Brassica oleraceaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Unk2QA [auth s]20Brassica oleraceaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
P1RA [auth m]98Brassica oleraceaMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
B12-1SA [auth t]73Brassica oleraceaMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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WA [auth I],
XA [auth I],
YA [auth J]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
T7X
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MB [auth p],
VA [auth I]
Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
U10
Query on U10

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ZA [auth H]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
NDP
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EB [auth T]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PEV
Query on PEV

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AB [auth H](1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
UA [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
BB [auth C]
CB [auth C]
HB [auth E]
IB [auth D]
JB [auth D]
BB [auth C],
CB [auth C],
HB [auth E],
IB [auth D],
JB [auth D],
TA [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
DB [auth C],
FB [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
GB [auth P],
KB [auth q]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
LB [auth q]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8

Structure Validation

View Full Validation Report



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