6RD8

CryoEM structure of Polytomella F-ATP synthase, c-ring position 2, focussed refinement of Fo and peripheral stalk


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F 1 -F o coupling.

Murphy, B.J.Klusch, N.Langer, J.Mills, D.J.Yildiz, O.Kuhlbrandt, W.

(2019) Science 364

  • DOI: 10.1126/science.aaw9128
  • Primary Citation of Related Structures:  
    6RDA, 6RDC, 6RDB, 6RDE, 6RDD, 6RDG, 6RDF, 6RD9, 6RD8, 6RD5, 6RD4, 6RD7, 6RD6, 6REB, 6REA, 6RED, 6REC, 6REF, 6REE, 6RDY, 6RDX, 6RE9, 6RDZ, 6RDQ, 6RE2, 6RDP, 6RE1, 6RDS, 6RE4, 6RDR, 6RE3, 6RDU, 6RE6, 6RDT, 6RE5, 6RDW, 6RE8, 6RDV, 6RE7, 6RDI, 6RDH, 6RDK, 6RDJ, 6RDM, 6RDL, 6RDO, 6RE0, 6RDN, 6RER, 6RET

  • PubMed Abstract: 
  • F 1 F o -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 Polytomella sp ...

    F 1 F o -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 Polytomella 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 c -ring rotation and result in ATP synthesis. Crucially, the F 1 head rotates along with the central stalk and c -ring rotor for the first ~30° of each 120° primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F 1 and F o 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 c -ring protonation with rotation.


    Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt 60438, Germany. werner.kuehlbrandt@biophys.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASA-10: Polytomella F-ATP synthase associated subunit 10A [auth 0]82Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5H1ZR95 (Polytomella sp. Pringsheim 198.80)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase associated protein ASA1B [auth 1]618Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: asa1
UniProt
Find proteins for Q85JD5 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial F1F0 ATP synthase associated 32 kDa proteinC [auth 3]325Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: asa3
UniProt
Find proteins for K0J903 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial F1F0 ATP synthase associated 14 kDa proteinD [auth 5]123Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: asa5
UniProt
Find proteins for A0A024FSR7 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ASA6E [auth 6]151Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for D7P897 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ASA8F [auth 8]89Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D8V7I7 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ASA-9: Polytomella F-ATP synthase associated subunit 9G [auth 9]97Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5H1ZR73 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit c127Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D7P7X5 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit 6R [auth M]327Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: atp6
Membrane Entity: Yes 
UniProt
Find proteins for H8PGG3 (Polytomella sp. Pringsheim 198.80)
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
S [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European Molecular Biology OrganizationGermanyALTF 702 2016

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence, Data collection, Data processing, Other
  • Version 1.2: 2020-09-30
    Changes: Database references