6RE3

Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2B, monomer-masked refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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

  • 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
Find similar proteins by:  (by identity cutoff)  |  Structure
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)
Explore A0A5H1ZR95 
Go to UniProtKB:  A0A5H1ZR95
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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)
Explore Q85JD5 
Go to UniProtKB:  Q85JD5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ASA-2: Polytomella F-ATP synthase associated subunit 2C [auth 2]441Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for D7P6B9 (Polytomella sp. Pringsheim 198.80)
Explore D7P6B9 
Go to UniProtKB:  D7P6B9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial F1F0 ATP synthase associated 32 kDa proteinD [auth 3]325Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: asa3
UniProt
Find proteins for K0J903 (Polytomella sp. Pringsheim 198.80)
Explore K0J903 
Go to UniProtKB:  K0J903
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase associated protein ASA4E [auth 4]294Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: asa4
UniProt
Find proteins for D7NIZ2 (Polytomella sp. Pringsheim 198.80)
Explore D7NIZ2 
Go to UniProtKB:  D7NIZ2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial F1F0 ATP synthase associated 14 kDa proteinF [auth 5]123Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: asa5
UniProt
Find proteins for A0A024FSR7 (Polytomella sp. Pringsheim 198.80)
Explore A0A024FSR7 
Go to UniProtKB:  A0A024FSR7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ASA6G [auth 6]151Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for D7P897 (Polytomella sp. Pringsheim 198.80)
Explore D7P897 
Go to UniProtKB:  D7P897
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase associated protein ASA7H [auth 7]190Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for D8V7I2 (Polytomella sp. Pringsheim 198.80)
Explore D8V7I2 
Go to UniProtKB:  D8V7I2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ASA8I [auth 8]89Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D8V7I7 (Polytomella sp. Pringsheim 198.80)
Explore D8V7I7 
Go to UniProtKB:  D8V7I7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ASA-9: Polytomella F-ATP synthase associated subunit 9J [auth 9]97Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5H1ZR73 (Polytomella sp. Pringsheim 198.80)
Explore A0A5H1ZR73 
Go to UniProtKB:  A0A5H1ZR73
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
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)
Explore D7P7X5 
Go to UniProtKB:  D7P7X5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit 6U [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)
Explore H8PGG3 
Go to UniProtKB:  H8PGG3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit OSCPV [auth P]229Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D8V7I1 (Polytomella sp. Pringsheim 198.80)
Explore D8V7I1 
Go to UniProtKB:  D8V7I1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
epsilon: Polytomella F-ATP synthase epsilon subunitW [auth Q]74Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A5H1ZR74 (Polytomella sp. Pringsheim 198.80)
Explore A0A5H1ZR74 
Go to UniProtKB:  A0A5H1ZR74
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit deltaX [auth R]199Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D7P7X6 (Polytomella sp. Pringsheim 198.80)
Explore D7P7X6 
Go to UniProtKB:  D7P7X6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase gamma chain, mitochondrialY [auth S]317Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: atp3
Membrane Entity: Yes 
UniProt
Find proteins for Q4LDE7 (Polytomella sp. Pringsheim 198.80)
Explore Q4LDE7 
Go to UniProtKB:  Q4LDE7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alphaZ [auth T], AA [auth U], BA [auth V]562Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: atp1
Membrane Entity: Yes 
UniProt
Find proteins for A0ZW40 (Polytomella sp. Pringsheim 198.80)
Explore A0ZW40 
Go to UniProtKB:  A0ZW40
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaCA [auth X], DA [auth Y], EA [auth Z]574Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Gene Names: atp2
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0ZW41 (Polytomella sp. Pringsheim 198.80)
Explore A0ZW41 
Go to UniProtKB:  A0ZW41
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
GA [auth T], IA [auth U], KA [auth V]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
MA [auth Y], OA [auth Z]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
HA [auth T], JA [auth U], LA [auth V], NA [auth Y], PA [auth Z]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




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: 2019-11-20
    Changes: Data collection, Data processing, Other
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2020-09-30
    Changes: Database references, Derived calculations