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- PDB-6rdj: Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate ... -

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Basic information

Entry
Database: PDB / ID: 6rdj
TitleCryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1A, focussed refinement of F1 head and rotor
Components
  • (ATP synthase subunit ...) x 2
  • (Mitochondrial ATP synthase subunit ...) x 3
  • ATP synthase gamma chain, mitochondrial
  • epsilon: Polytomella F-ATP synthase epsilon subunit
KeywordsPROTON TRANSPORT / mitochondrial ATP synthase dimer flexible coupling cryoEM
Function / homology
Function and homology information


proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / mitochondrial inner membrane ...proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / membrane
Similarity search - Function
ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, epsilon subunit, mitochondrial ...ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / epsilon: Polytomella F-ATP synthase epsilon subunit / ATP synthase subunit alpha / ATP synthase subunit beta / Mitochondrial ATP synthase subunit c / Mitochondrial ATP synthase subunit delta / Mitochondrial ATP synthase subunit OSCP / F-ATPase gamma subunit
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMurphy, B.J. / Klusch, N. / Yildiz, O. / Kuhlbrandt, W.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
European Molecular Biology OrganizationALTF 702 2016 Germany
CitationJournal: Science / Year: 2019
Title: Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F-F coupling.
Authors: Bonnie J Murphy / Niklas Klusch / Julian Langer / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt /
Abstract: FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy ...FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy structure of active dimeric ATP synthase from mitochondria of sp. at a resolution of 2.7 to 2.8 angstroms. Separation of 13 well-defined rotary substates by three-dimensional classification provides a detailed picture of the molecular motions that accompany -ring rotation and result in ATP synthesis. Crucially, the F head rotates along with the central stalk and -ring rotor for the first ~30° of each 120° primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F and F subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit. A conserved metal ion in the proton access channel may synchronize -ring protonation with rotation.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Data processing / Other
Category: atom_sites / em_ctf_correction ...atom_sites / em_ctf_correction / em_image_processing / em_imaging / em_imaging_optics / em_particle_selection / em_single_particle_entity
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _em_ctf_correction.details / _em_image_processing.details / _em_imaging.details / _em_imaging_optics.chr_aberration_corrector / _em_imaging_optics.phase_plate / _em_imaging_optics.sph_aberration_corrector / _em_particle_selection.details
Revision 1.2Sep 30, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.title / _struct_conn.pdbx_dist_value ..._citation.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
P: Mitochondrial ATP synthase subunit OSCP
Q: epsilon: Polytomella F-ATP synthase epsilon subunit
R: Mitochondrial ATP synthase subunit delta
S: ATP synthase gamma chain, mitochondrial
T: ATP synthase subunit alpha
U: ATP synthase subunit alpha
V: ATP synthase subunit alpha
X: ATP synthase subunit beta
Y: ATP synthase subunit beta
Z: ATP synthase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)586,51030
Polymers584,01220
Non-polymers2,49710
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area95820 Å2
ΔGint-698 kcal/mol
Surface area148530 Å2
MethodPISA

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Components

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Mitochondrial ATP synthase subunit ... , 3 types, 12 molecules ABCDEFGHIJPR

#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 OSCP


Mass: 25530.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D8V7I1
#4: Protein Mitochondrial ATP synthase subunit delta


Mass: 20880.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D7P7X6

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Protein , 2 types, 2 molecules QS

#3: Protein epsilon: Polytomella F-ATP synthase epsilon subunit


Mass: 8205.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A5H1ZR74*PLUS
#5: Protein ATP synthase gamma chain, mitochondrial


Mass: 34639.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: Q4LDE7

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ATP synthase subunit ... , 2 types, 6 molecules TUVXYZ

#6: Protein ATP synthase subunit alpha


Mass: 60766.152 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0ZW40
#7: Protein ATP synthase subunit beta


Mass: 61939.070 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant)
References: UniProt: A0ZW41, H+-transporting two-sector ATPase

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Non-polymers , 3 types, 10 molecules

#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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 F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 1.6 MDa / Experimental value: NO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Buffer solutionpH: 7.8
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: 75000 X / Nominal defocus max: -5000 nm / Nominal defocus min: -400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 3840 / Height: 3712

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
4CTFFIND4.1.10CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.14model refinement
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 735197
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124537 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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