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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4102 | ||||||||||||
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Title | Structure of F-ATPase from Pichia angusta, state1 | ||||||||||||
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![]() | ATP synthase / hydrolase | ||||||||||||
Function / homology | ![]() angiostatin binding / ATPase inhibitor activity / negative regulation of hydrolase activity / heme biosynthetic process / : / : / : / : / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) ...angiostatin binding / ATPase inhibitor activity / negative regulation of hydrolase activity / heme biosynthetic process / : / : / : / : / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial nucleoid / : / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / 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 / erythrocyte differentiation / mitochondrial membrane / ADP binding / ATPase binding / protein homotetramerization / membrane => GO:0016020 / calmodulin binding / hydrolase activity / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | ||||||||||||
![]() | Vinothkumar KR / Montgomery MG | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the mitochondrial ATP synthase from determined by electron cryo-microscopy. Authors: Kutti R Vinothkumar / Martin G Montgomery / Sidong Liu / John E Walker / ![]() Abstract: The structure of the intact monomeric ATP synthase from the fungus, , has been solved by electron cryo-microscopy. The structure provides insights into the mechanical coupling of the transmembrane ...The structure of the intact monomeric ATP synthase from the fungus, , has been solved by electron cryo-microscopy. The structure provides insights into the mechanical coupling of the transmembrane proton motive force across mitochondrial membranes in the synthesis of ATP. This mechanism requires a strong and integral stator, consisting of the catalytic αβ-domain, peripheral stalk, and, in the membrane domain, subunit a and associated supernumerary subunits, kept in contact with the rotor turning at speeds up to 350 Hz. The stator's integrity is ensured by robust attachment of both the oligomycin sensitivity conferral protein (OSCP) to the catalytic domain and the membrane domain of subunit b to subunit a. The ATP8 subunit provides an additional brace between the peripheral stalk and subunit a. At the junction between the OSCP and the apparently stiff, elongated α-helical b-subunit and associated d- and h-subunits, an elbow or joint allows the stator to bend to accommodate lateral movements during the activity of the catalytic domain. The stator may also apply lateral force to help keep the static a-subunit and rotating c-ring together. The interface between the c-ring and the a-subunit contains the transmembrane pathway for protons, and their passage across the membrane generates the turning of the rotor. The pathway has two half-channels containing conserved polar residues provided by a bundle of four α-helices inclined at ∼30° to the plane of the membrane, similar to those described in other species. The structure provides more insights into the workings of this amazing machine. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 91.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.3 KB 31.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.4 KB | Display | ![]() |
Images | ![]() | 52.6 KB | ||
Filedesc metadata | ![]() | 8.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lqzMC ![]() 4100C ![]() 4101C ![]() 5lqxC ![]() 5lqyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.75 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Yeast F1FO ATP Synthase
+Supramolecule #1: Yeast F1FO ATP Synthase
+Macromolecule #1: ATP synthase subunit f
+Macromolecule #2: ATP synthase subunit AAP1
+Macromolecule #3: ATP synthase subunit a
+Macromolecule #4: ATP synthase subunit b
+Macromolecule #5: ATP synthase alpha subunit
+Macromolecule #6: ATP synthase beta subunit
+Macromolecule #7: ATP synthase gamma subunit
+Macromolecule #8: ATP synthase delta subunit
+Macromolecule #9: ATP synthase epsilon subunit
+Macromolecule #10: ATP synthase inhibitor protein IF1
+Macromolecule #11: ATP synthase subunit c
+Macromolecule #12: ATP synthase OSCP subunit
+Macromolecule #13: ATP synthase subunit b
+Macromolecule #14: ATP synthase subunit d
+Macromolecule #15: ATP synthase subunit h
+Macromolecule #16: ATP synthase subunit a
+Macromolecule #17: ATP synthase subunit a
+Macromolecule #18: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #19: MAGNESIUM ION
+Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER Details: Grids were blotted for 12-14 seconds before plunging.. | ||||||||||||
Details | The enzyme with bound inhibitor protein extracted and purified in Cymal-7. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 87.5 K |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-32 / Average exposure time: 4.0 sec. / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 81395 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | The refinement of whole data was done at 1.72 A sampling. The map was scaled to 1.75 A after comparison with the model. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5lqz: |