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- PDB-8bee: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

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Basic information

Entry
Database: PDB / ID: 8bee
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 3
  • (Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 2
  • Acyl carrier protein 2, mitochondrial
  • NADH dehydrogenase subunit 7
KeywordsMEMBRANE PROTEIN / Plant / Mitochondria / Complex
Function / homology
Function and homology information


photorespiration / embryo development ending in seed dormancy / cobalt ion binding / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding ...photorespiration / embryo development ending in seed dormancy / cobalt ion binding / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / proton transmembrane transport / respiratory electron transport chain / mitochondrial membrane / NAD binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / extracellular region / zinc ion binding / metal ion binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / GRIM-19 / GRIM-19 protein / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 ...Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / GRIM-19 / GRIM-19 protein / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Acyl carrier protein (ACP) / 4Fe-4S dicluster domain / Phosphopantetheine attachment site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Phosphopantetheine attachment site. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8Q1 / Chem-NDP / IRON/SULFUR CLUSTER / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / Acyl carrier protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial ...Chem-8Q1 / Chem-NDP / IRON/SULFUR CLUSTER / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / Acyl carrier protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsKlusch, N. / Kuehlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Authors: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
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 ...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.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
D: NADH dehydrogenase subunit 7
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
U: Acyl carrier protein 2, mitochondrial
V: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
q: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,86615
Polymers244,52510
Non-polymers2,3415
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33440 Å2
ΔGint-182 kcal/mol
Surface area63560 Å2
MethodPISA

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Components

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 3 types, 3 molecules BCI

#1: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 24071.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42577, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH dehydrogenase subunit 9


Mass: 22910.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q95748, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial


Mass: 25536.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q42599, NADH:ubiquinone reductase (H+-translocating)

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Protein , 2 types, 2 molecules DU

#3: Protein NADH dehydrogenase subunit 7


Mass: 45036.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A2P2CLH2
#6: Protein Acyl carrier protein 2, mitochondrial / MtACP-2 / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 14183.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O80800

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 3 types, 3 molecules PWZ

#5: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial


Mass: 43988.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SK66
#8: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 15102.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LHI0
#9: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Protein MATERNAL EFFECT EMBRYO ARREST 4


Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RWA7

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Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 2 types, 2 molecules Vq

#7: Protein Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial


Mass: 19201.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLX7
#10: Protein Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 18346.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M9M9

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Non-polymers , 4 types, 636 molecules

#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)
Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenConc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
5CTFFIND4.1.13CTF correction
8Coot0.9.5model fitting
9RELION3.1.3initial Euler assignment
10RELION3.1.3classification
11RELION3.1.33D reconstruction
12PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1215138
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213993 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413475
ELECTRON MICROSCOPYf_angle_d0.63718282
ELECTRON MICROSCOPYf_dihedral_angle_d6.2751817
ELECTRON MICROSCOPYf_chiral_restr0.0451986
ELECTRON MICROSCOPYf_plane_restr0.0052354

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