[English] 日本語
![](img/lk-miru.gif)
- EMDB-4826: Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-4826 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1C, focussed refinement of F1 head and rotor | |||||||||
![]() | None | |||||||||
![]() |
| |||||||||
![]() | mitochondrial ATP synthase dimer flexible coupling cryoEM / PROTON TRANSPORT | |||||||||
Function / homology | ![]() : / : / : / : / photosynthetic electron transport in photosystem I / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis ...: / : / : / : / photosynthetic electron transport in photosystem I / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Murphy BJ / Klusch N | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 395.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 23.4 KB 23.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.9 KB | Display | ![]() |
Images | ![]() | 176.9 KB | ||
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() | 337.9 MB 337.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rdpMC ![]() 4805C ![]() 4806C ![]() 4807C ![]() 4808C ![]() 4809C ![]() 4810C ![]() 4811C ![]() 4812C ![]() 4813C ![]() 4814C ![]() 4815C ![]() 4816C ![]() 4817C ![]() 4818C ![]() 4819C ![]() 4820C ![]() 4821C ![]() 4822C ![]() 4823C ![]() 4824C ![]() 4825C ![]() 4827C ![]() 4828C ![]() 4829C ![]() 4830C ![]() 4831C ![]() 4832C ![]() 4833C ![]() 4834C ![]() 4835C ![]() 4836C ![]() 4837C ![]() 4838C ![]() 4839C ![]() 4840C ![]() 4841C ![]() 4842C ![]() 4843C ![]() 4844C ![]() 4845C ![]() 4846C ![]() 4847C ![]() 4848C ![]() 4849C ![]() 4850C ![]() 4851C ![]() 4852C ![]() 4853C ![]() 4854C ![]() 4855C ![]() 4856C ![]() 4857C ![]() 6rd4C ![]() 6rd5C ![]() 6rd6C ![]() 6rd7C ![]() 6rd8C ![]() 6rd9C ![]() 6rdaC ![]() 6rdbC ![]() 6rdcC ![]() 6rddC ![]() 6rdeC ![]() 6rdfC ![]() 6rdgC ![]() 6rdhC ![]() 6rdiC ![]() 6rdjC ![]() 6rdkC ![]() 6rdlC ![]() 6rdmC ![]() 6rdnC ![]() 6rdoC ![]() 6rdqC ![]() 6rdrC ![]() 6rdsC ![]() 6rdtC ![]() 6rduC ![]() 6rdvC ![]() 6rdwC ![]() 6rdxC ![]() 6rdyC ![]() 6rdzC ![]() 6re0C ![]() 6re1C ![]() 6re2C ![]() 6re3C ![]() 6re4C ![]() 6re5C ![]() 6re6C ![]() 6re7C ![]() 6re8C ![]() 6re9C ![]() 6reaC ![]() 6rebC ![]() 6recC ![]() 6redC ![]() 6reeC ![]() 6refC ![]() 6repC ![]() 6rerC ![]() 6resC ![]() 6retC ![]() 6reuC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | |
EM raw data | ![]() Data size: 43.8 TB Data #1: Unaligned frames, gain reference corrected [micrographs - multiframe]) |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.053 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: None
File | emd_4826_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: None
File | emd_4826_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : Polytomella F-ATP synthase
+Supramolecule #1: Polytomella F-ATP synthase
+Macromolecule #1: Mitochondrial ATP synthase subunit c
+Macromolecule #2: Mitochondrial ATP synthase subunit OSCP
+Macromolecule #3: epsilon: Polytomella F-ATP synthase epsilon subunit
+Macromolecule #4: Mitochondrial ATP synthase subunit delta
+Macromolecule #5: ATP synthase gamma chain, mitochondrial
+Macromolecule #6: ATP synthase subunit alpha
+Macromolecule #7: ATP synthase subunit beta
+Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 3.5 mg/mL |
---|---|
Buffer | pH: 7.8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -5.0 µm / Nominal defocus min: -0.4 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | ![]() PDB-6rdp: |