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Structure paper

TitleRotary substates of mitochondrial ATP synthase reveal the basis of flexible F-F coupling.
Journal, issue, pagesScience, Vol. 364, Issue 6446, Year 2019
Publish dateJun 21, 2019
AuthorsBonnie J Murphy / Niklas Klusch / Julian Langer / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt /
PubMed AbstractFF-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.
External linksScience / PubMed:31221832
MethodsEM (single particle)
Resolution2.69 - 4.3 Å
Structure data

EMDB-4805, PDB-6rd4:
CryoEM structure of Polytomella F-ATP synthase, Full dimer, composite map
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-4806, PDB-6rd5:
CryoEM structure of Polytomella F-ATP synthase, focussed refinement of Fo and peripheral stalk, C2 symmetry
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-4807, PDB-6rd6:
CryoEM structure of Polytomella F-ATP synthase, focussed refinement of upper peripheral stalk
Method: EM (single particle) / Resolution: 2.75 Å

EMDB-4808, PDB-6rd7:
CryoEM structure of Polytomella F-ATP synthase, c-ring position 1, focussed refinement of Fo and peripheral stalk
Method: EM (single particle) / Resolution: 2.73 Å

EMDB-4809, PDB-6rd8:
CryoEM structure of Polytomella F-ATP synthase, c-ring position 2, focussed refinement of Fo and peripheral stalk
Method: EM (single particle) / Resolution: 3.08 Å

EMDB-4810, PDB-6rd9:
CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 1, composite map
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-4811, PDB-6rda:
CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 1, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-4812, PDB-6rdb:
CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 1, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-4813, PDB-6rdc:
CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 2, composite map
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4814, PDB-6rdd:
Cryo-EM structure of Polytomella F-ATP synthase, Primary rotary state 2, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4815, PDB-6rde:
CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 2, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-4816, PDB-6rdf:
CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 3, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4817, PDB-6rdg:
CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 3, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-4818, PDB-6rdh:
CryoEM structure of Polytomella F-ATP synthase, Rotary substate 1A, composite map
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-4819, PDB-6rdi:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1A, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4820, PDB-6rdj:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1A, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-4821, PDB-6rdk:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-4822, PDB-6rdl:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-4823, PDB-6rdm:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.44 Å

EMDB-4824, PDB-6rdn:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1C, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4825, PDB-6rdo:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1C, composite map
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-4826, PDB-6rdp:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1C, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-4827, PDB-6rdq:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1D, composite map
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-4828, PDB-6rdr:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1D, monomer-masked refinement
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-4829, PDB-6rds:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1D, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-4830, PDB-6rdt:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1E, composite map
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-4831, PDB-6rdu:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1E, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-4832, PDB-6rdv:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1E, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-4833, PDB-6rdw:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1F, composite map
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-4834, PDB-6rdx:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1F, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-4835, PDB-6rdy:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1F, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-4836, PDB-6rdz:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2A, composite map
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-4837, PDB-6re0:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2A, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-4838, PDB-6re1:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2A, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4839, PDB-6re2:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2B, composite map
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4840, PDB-6re3:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2B, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-4841, PDB-6re4:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2B, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-4842, PDB-6re5:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2C, composite map
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4843, PDB-6re6:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2C, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-4844, PDB-6re7:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2C, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-4845, PDB-6re8:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2D, composite map
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-4846, PDB-6re9:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2D, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-4847, PDB-6rea:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 2D, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-4848, PDB-6reb:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3A, composite map
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-4849, PDB-6rec:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3A, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-4850, PDB-6red:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3A, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-4851, PDB-6ree:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3B, composite map
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-4852, PDB-6ref:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3B, monomer-masked refinement
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-4853, PDB-6rep:
Cryo-EM structure of Polytomella F-ATP synthase, Primary rotary state 3, composite map
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-4854, PDB-6rer:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3B, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-4855, PDB-6res:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3C, composite map
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-4856, PDB-6ret:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3C, monomer-masked refinement
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-4857, PDB-6reu:
Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 3C, focussed refinement of F1 head and rotor
Method: EM (single particle) / Resolution: 4.2 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-HOH:
WATER

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

Source
  • polytomella sp. pringsheim 198.80 (plant)
KeywordsPROTON TRANSPORT / mitochondrial ATP synthase dimer flexible coupling cryoEM

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