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- PDB-5lqy: Structure of F-ATPase from Pichia angusta, state2 -

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Entry
Database: PDB / ID: 5lqy
TitleStructure of F-ATPase from Pichia angusta, state2
Descriptor(ATP synthase ...) x 14
KeywordsHYDROLASE / ATP synthase / ATP hydrolase / complex / hydrolase
Specimen sourceBos taurus / mammal / Bovine / ウシ /
Ogataea angusta / fungus
MethodElectron microscopy (7.8 Å resolution / Particle / Single particle)
AuthorsVinothkumar, K.R. / Montgomery, M.G. / Liu, S. / Walker, J.E.
CitationProc. Natl. Acad. Sci. U.S.A., 2016

Proc. Natl. Acad. Sci. U.S.A., 2016 StrPapers
Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.
Kutti R Vinothkumar / Martin G Montgomery / Sidong Liu / John E Walker

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 17, 2016 / Release: Nov 16, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 16, 2016Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Experimental preparationem_sample_support / em_software_em_sample_support.grid_type / _em_software.name

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Assembly

Deposited unit
1: ATP synthase subunit f
2: ATP synthase subunit AAP1
3: ATP synthase subunit a
4: ATP synthase subunit b
A: ATP synthase alpha subunit
B: ATP synthase alpha subunit
C: ATP synthase alpha subunit
D: ATP synthase beta subunit
E: ATP synthase beta subunit
F: ATP synthase beta subunit
G: ATP synthase gamma subunit
H: ATP synthase delta subunit
I: ATP synthase epsilon subunit
J: ATP synthase inhibitor protein IF1
K: ATP synthase c subunit
L: ATP synthase c subunit
M: ATP synthase c subunit
N: ATP synthase c subunit
O: ATP synthase c subunit
P: ATP synthase c subunit
Q: ATP synthase c subunit
R: ATP synthase c subunit
S: ATP synthase c subunit
T: ATP synthase c subunit
U: ATP synthase OSCP subunit
V: ATP synthase subunit b
W: ATP synthase subunit d
X: ATP synthase subunit h
Y: ATP synthase subunit a
Z: ATP synthase subunit a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)557,70541
Polyers554,94130
Non-polymers2,76511
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 17 types, 30 molecules 1234ABCDEF...

#1: Polypeptide(L)ATP synthase subunit f


Mass: 2571.161 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta
#2: Polypeptide(L)ATP synthase subunit AAP1


Mass: 2145.636 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta
#3: Polypeptide(L)ATP synthase subunit a


Mass: 1464.797 Da / Num. of mol.: 1 / Details: Helix 1 of subunit a / Source: (natural) Ogataea angusta
#4: Polypeptide(L)ATP synthase subunit b


Mass: 2315.846 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta
#5: Polypeptide(L)ATP synthase alpha subunit


Mass: 55007.535 Da / Num. of mol.: 3 / Source: (natural) Ogataea angusta

Cellular component

  • mitochondrial nucleoid (GO: 0042645)
  • mitochondrial proton-transporting ATP synthase, catalytic core (GO: 0005754)

Molecular function

Biological process

#6: Polypeptide(L)ATP synthase beta subunit


Mass: 50852.434 Da / Num. of mol.: 3 / Source: (natural) Ogataea angusta

Cellular component

  • proton-transporting ATP synthase complex, catalytic core F(1) (GO: 0045261)

Molecular function

Biological process

#7: Polypeptide(L)ATP synthase gamma subunit


Mass: 29418.238 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta

Cellular component

  • mitochondrial proton-transporting ATP synthase, central stalk (GO: 0005756)

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)
  • proton-transporting ATPase activity, rotational mechanism (GO: 0046961)

Biological process

#8: Polypeptide(L)ATP synthase delta subunit


Mass: 14171.783 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta

Cellular component

  • mitochondrial proton-transporting ATP synthase, central stalk (GO: 0005756)

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)

Biological process

#9: Polypeptide(L)ATP synthase epsilon subunit


Mass: 6910.886 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta

Cellular component

  • mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO: 0000275)

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)

Biological process

#10: Polypeptide(L)ATP synthase inhibitor protein IF1


Mass: 7462.098 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)
ATP synthase c subunit


Mass: 7837.380 Da / Num. of mol.: 10 / Source: (natural) Ogataea angusta

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)ATP synthase OSCP subunit


Mass: 20678.812 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta

Cellular component

  • mitochondrial proton-transporting ATP synthase, stator stalk (GO: 0000274)

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)

Biological process

#13: Polypeptide(L)ATP synthase subunit b


Mass: 22292.332 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta

Cellular component

  • integral component of membrane (GO: 0016021)
  • mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO: 0000276)

Molecular function

  • hydrogen ion transmembrane transporter activity (GO: 0015078)

Biological process

#14: Polypeptide(L)ATP synthase subunit d


Mass: 16427.818 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta

Cellular component

  • mitochondrial proton-transporting ATP synthase, stator stalk (GO: 0000274)

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)

Biological process

#15: Polypeptide(L)ATP synthase subunit h


Mass: 1805.216 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta
#16: Polypeptide(L)ATP synthase subunit a


Mass: 27559.775 Da / Num. of mol.: 1 / Details: helices 4, 5 and 6 / Source: (natural) Ogataea angusta

Cellular component

Molecular function

  • hydrogen ion transmembrane transporter activity (GO: 0015078)

Biological process

#17: Polypeptide(L)ATP synthase subunit a


Mass: 3762.629 Da / Num. of mol.: 1 / Details: Helices 2 and 3 of subunit a / Source: (natural) Ogataea angusta

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Non-polymers , 3 types, 11 molecules

#18: ChemicalChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3
#19: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg
#20: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Yeast F1FO ATP Synthase / Type: COMPLEX
Details: The complex comprises of the catalytic domain, membrane domain and peripheral stalk of the yeast ATP synthase.
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17
Source: NATURAL
Molecular weightValue: 0.55 deg. / Units: MEGADALTONS
Source (natural)Organism: Ogataea angusta
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameBuffer ID
120mMTris-HCL1
2100mMsodium chloride1
32mMMagnesium sulphate1
42mMATP1
50.05%Cymal-71
SpecimenConc.: 3.5 mg/ml
Details: The enzyme with bound inhibitor protein extracted in DDM and purified in Cymal-7.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R0.6/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins
Details: Grids were blotted for 12-14 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 / Calibrated magnification: 81395 / Nominal defocus max: 5000 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 87.5 kelvins
Image recordingAverage exposure time: 4 sec. / Electron dose: 64 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 microns / Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 69 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategoryDetailsImage processing IDImaging IDFitting ID
1RELION1.4PARTICLE SELECTIONUsing template generated with a subset of data, particles were automatically picked, followed by manual inspection and deletion of aggregates and non-particles.1
2EPUIMAGE ACQUISITIONOne image was collected for each hole1
4CTFFIND3CTF CORRECTIONCTF correction was applied to each particle in RELION1
7Coot0.8.3MODEL FITTING1
12RELION1.4CLASSIFICATION1
13RELION1.4RECONSTRUCTION1
Image processingDetails: The total exposure was 4 seconds resulting in 69 frames and a total dose of 64 e/A2. Frames were captured with an in-house protocol. For processing frames 1-32 were used.
CTF correctionType: NONE
Particle selectionDetails: After 2D classification, the number of particles used for orientation determination and reconstruction was 100724 particles followed by per-particle motion correction and B-factor weighting.
Number of particles selected: 123683
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 23065 / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingDetails: 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.
Ref protocol: RIGID BODY FIT / Ref space: REAL

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