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- PDB-6rd5: CryoEM structure of Polytomella F-ATP synthase, focussed refineme... -

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Basic information

Entry
Database: PDB / ID: 6rd5
TitleCryoEM structure of Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
Components
  • (Mitochondrial ATP synthase subunit ...) x 4
  • (Mitochondrial F1F0 ATP synthase associated ...) x 2
  • ASA-10: Polytomella F-ATP synthase associated subunit 10
  • ATP synthase associated protein ASA1
KeywordsPROTON TRANSPORT / mitochondrial ATP synthase dimer flexible coupling cryoEM
Function / homology
Function and homology information


: / proton-transporting ATP synthase activity, rotational mechanism / mitochondrion / membrane
Similarity search - Function
: / F1F0 ATP synthase subunit ASA5 / 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.
Similarity search - Domain/homology
Chem-PEV / Mitochondrial F1F0 ATP synthase associated 14 kDa protein / ASA-9: Polytomella F-ATP synthase associated subunit 9 / ASA-10: Polytomella F-ATP synthase associated subunit 10 / Mitochondrial ATP synthase subunit ASA6 / Mitochondrial ATP synthase subunit ASA8 / F-ATPase protein 6 / Mitochondrial F1F0 ATP synthase associated 32 kDa protein / ATP synthase associated protein ASA1
Similarity search - Component
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 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 1.1Jul 10, 2019Group: Data collection / Derived calculations
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _em_admin.last_update / _pdbx_struct_assembly.oligomeric_count ..._em_admin.last_update / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Dec 18, 2019Group: 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
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 1.3Sep 30, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4May 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
0: ASA-10: Polytomella F-ATP synthase associated subunit 10
1: ATP synthase associated protein ASA1
3: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
5: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
6: Mitochondrial ATP synthase subunit ASA6
8: Mitochondrial ATP synthase subunit ASA8
9: Mitochondrial ATP synthase subunit ASA9
M: Mitochondrial ATP synthase subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,92928
Polymers197,8588
Non-polymers12,07020
Water99155
1
0: ASA-10: Polytomella F-ATP synthase associated subunit 10
1: ATP synthase associated protein ASA1
3: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
5: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
6: Mitochondrial ATP synthase subunit ASA6
8: Mitochondrial ATP synthase subunit ASA8
9: Mitochondrial ATP synthase subunit ASA9
M: Mitochondrial ATP synthase subunit 6
hetero molecules

0: ASA-10: Polytomella F-ATP synthase associated subunit 10
1: ATP synthase associated protein ASA1
3: Mitochondrial F1F0 ATP synthase associated 32 kDa protein
5: Mitochondrial F1F0 ATP synthase associated 14 kDa protein
6: Mitochondrial ATP synthase subunit ASA6
8: Mitochondrial ATP synthase subunit ASA8
9: Mitochondrial ATP synthase subunit ASA9
M: Mitochondrial ATP synthase subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,85756
Polymers395,71616
Non-polymers24,14140
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1

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Components

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Protein , 2 types, 2 molecules 01

#1: Protein ASA-10: Polytomella F-ATP synthase associated subunit 10


Mass: 8731.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A5H1ZR95*PLUS
#2: Protein ATP synthase associated protein ASA1


Mass: 68679.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: Q85JD5

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Mitochondrial F1F0 ATP synthase associated ... , 2 types, 2 molecules 35

#3: Protein Mitochondrial F1F0 ATP synthase associated 32 kDa protein


Mass: 34850.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: K0J903
#4: Protein Mitochondrial F1F0 ATP synthase associated 14 kDa protein


Mass: 14004.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A024FSR7

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Mitochondrial ATP synthase subunit ... , 4 types, 4 molecules 689M

#5: 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
#6: Protein Mitochondrial ATP synthase subunit ASA8


Mass: 9883.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: D8V7I7
#7: Protein Mitochondrial ATP synthase subunit ASA9


Mass: 11001.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) / References: UniProt: A0A5H1ZR73*PLUS
#8: 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

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Sugars , 1 types, 8 molecules

#10: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 67 molecules

#9: Chemical
ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM
#11: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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 F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
Type: COMPLEX
Details: Generated by focussed refinement of the Fo and peripheral stalk region, with C2 symmetry applied
Entity ID: #1-#8 / Source: NATURAL
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

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
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
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 388670 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

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