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

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Entry
Database: PDB / ID: 5lqy
TitleStructure of F-ATPase from Pichia angusta, in 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 Yorodumi Papers
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
1.2Jan 24, 2018Structure modelSource and taxonomyentity_src_gen_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
1.3Jan 31, 2018Structure modelStructure summarystruct_struct.title

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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

Component

Type: COMPLEX

IDNameDetailsEntity IDParent IDSource
1Yeast F1FO ATP SynthaseThe complex comprises of the catalytic domain, membrane domain and peripheral stalk of the yeast ATP synthase.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 170MULTIPLE SOURCES
2Yeast F1FO ATP SynthaseYeast F1FO ATP Synthase1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 171NATURAL
3ATP synthase inhibitor protein IF1ATP synthase inhibitor protein IF1101RECOMBINANT
Molecular weightValue: 0.55 deg. / Units: MEGADALTONS
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
22870730Ogataea angusta
339913Bos taurus
Source (recombinant)Organism: Escherichia coli BL21(DE3)
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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