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- PDB-7arc: Cryo-EM structure of Polytomella Complex-I (peripheral arm) -

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Basic information

Entry
Database: PDB / ID: 7arc
TitleCryo-EM structure of Polytomella Complex-I (peripheral arm)
Components
  • 13 kDa
  • 18 kDa
  • 24 kDa
  • 39 kDa
  • 51 kDa
  • 75 kDa
  • B13
  • B14
  • B14.5a
  • B17.2
  • B8
  • ND7
  • ND9
  • PSST
  • SDAP2
  • TYKY
KeywordsELECTRON TRANSPORT / Complex-I
Function / homology
Function and homology information


NADH:ubiquinone oxidoreductase Nqo5 subunit / Rossmann fold - #12280 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Beta Polymerase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich ...NADH:ubiquinone oxidoreductase Nqo5 subunit / Rossmann fold - #12280 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Beta Polymerase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8Q1 / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKlusch, N. / Kuehlbrandt, W. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 8, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 8, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
B: PSST
C: ND9
D: ND7
E: 24 kDa
F: 51 kDa
G: 75 kDa
I: TYKY
P: 39 kDa
Q: 18 kDa
R: 13 kDa
S: B8
U: SDAP2
V: B13
W: B14
q: B17.2
r: B14.5a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,83328
Polymers440,56416
Non-polymers4,26912
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 16 types, 16 molecules BCDEFGIPQRSUVWqr

#1: Protein PSST


Mass: 18158.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#2: Protein ND9


Mass: 25689.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#3: Protein ND7


Mass: 45263.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#4: Protein 24 kDa


Mass: 30186.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#5: Protein 51 kDa


Mass: 51593.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#6: Protein 75 kDa


Mass: 77364.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#7: Protein TYKY


Mass: 26140.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#8: Protein 39 kDa


Mass: 41233.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#9: Protein 18 kDa


Mass: 20800.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#10: Protein 13 kDa


Mass: 14346.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#11: Protein B8


Mass: 10509.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#12: Protein SDAP2


Mass: 13393.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#13: Protein B13


Mass: 17745.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#14: Protein B14


Mass: 16134.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#15: Protein B17.2


Mass: 18178.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
#16: Protein B14.5a


Mass: 13827.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)

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Non-polymers , 7 types, 430 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#19: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#20: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#22: 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
#23: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: Polytomella complex I - Peripheral arm / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42350 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.58 Å2

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