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- PDB-6f36: Polytomella Fo model -

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Basic information

Entry
Database: PDB / ID: 6f36
TitlePolytomella Fo model
Components
  • Mitochondrial ATP synthase subunit 6
  • Mitochondrial ATP synthase subunit ASA6
  • Mitochondrial ATP synthase subunit c
KeywordsPROTON TRANSPORT / electron cryo-microscopy mitochondrial ATP synthase membrane protein energy conversion proton pathway
Function / homology
Function and homology information


thylakoid / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / intracellular membrane-bounded organelle / lipid binding / cytoplasm
Similarity search - Function
F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily ...F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial ATP synthase subunit c / Mitochondrial ATP synthase subunit ASA6 / F-ATPase protein 6
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYildiz, O. / Kuehlbrandt, W. / Klusch, N. / Murphy, B.J. / Mills, D.J.
Funding support Germany, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research FoundationSFB807 Germany
European Molecular Biology Organization Germany
CitationJournal: Elife / Year: 2017
Title: Structural basis of proton translocation and force generation in mitochondrial ATP synthase.
Authors: Niklas Klusch / Bonnie J Murphy / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt /
Abstract: ATP synthases produce ATP by rotary catalysis, powered by the electrochemical proton gradient across the membrane. Understanding this fundamental process requires an atomic model of the proton ...ATP synthases produce ATP by rotary catalysis, powered by the electrochemical proton gradient across the membrane. Understanding this fundamental process requires an atomic model of the proton pathway. We determined the structure of an intact mitochondrial ATP synthase dimer by electron cryo-microscopy at near-atomic resolution. Charged and polar residues of the -subunit stator define two aqueous channels, each spanning one half of the membrane. Passing through a conserved membrane-intrinsic helix hairpin, the lumenal channel protonates an acidic glutamate in the -ring rotor. Upon ring rotation, the protonated glutamate encounters the matrix channel and deprotonates. An arginine between the two channels prevents proton leakage. The steep potential gradient over the sub-nm inter-channel distance exerts a force on the deprotonated glutamate, resulting in net directional rotation.
History
DepositionNov 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Data processing / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
A: Mitochondrial ATP synthase subunit c
B: Mitochondrial ATP synthase subunit c
C: Mitochondrial ATP synthase subunit c
D: Mitochondrial ATP synthase subunit c
E: Mitochondrial ATP synthase subunit c
F: Mitochondrial ATP synthase subunit c
G: Mitochondrial ATP synthase subunit c
H: Mitochondrial ATP synthase subunit c
I: Mitochondrial ATP synthase subunit c
J: Mitochondrial ATP synthase subunit c
M: Mitochondrial ATP synthase subunit 6
N: Mitochondrial ATP synthase subunit ASA6


Theoretical massNumber of molelcules
Total (without water)177,34712
Polymers177,34712
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35270 Å2
ΔGint-385 kcal/mol
Surface area42100 Å2
MethodPISA

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Components

#1: Protein
Mitochondrial ATP synthase subunit c


Mass: 12664.013 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7P7X5
#2: Protein Mitochondrial ATP synthase subunit 6


Mass: 34802.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: H8PGG3
#3: Protein Mitochondrial ATP synthase subunit ASA6


Mass: 15904.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7P897

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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: Polytommella mitochondrial ATP synthase Fo complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 282 K

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 82 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 30
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 45 / Used frames/image: 1-45

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN2particle selection
4CTFFIND4CTF correction
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90142 / Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0097582
ELECTRON MICROSCOPYf_angle_d1.09310289
ELECTRON MICROSCOPYf_dihedral_angle_d12.0454350
ELECTRON MICROSCOPYf_chiral_restr0.0651286
ELECTRON MICROSCOPYf_plane_restr0.0071259

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