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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
Components(ATP synthase ...) x 17
KeywordsHYDROLASE / ATP synthase / ATP hydrolase / complex / hydrolase
Function / homologyATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A / ATPase, OSCP/delta subunit / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain ...ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A / ATPase, OSCP/delta subunit / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, beta subunit / Mitochondrial ATPase inhibitor / ATP synthase, F0 complex, subunit D, mitochondrial / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit A, active site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F1 complex, gamma subunit conserved site / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F0 complex, subunit A superfamily / F/V-ATP synthase subunit C superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase alpha and beta subunits signature. / ATP synthase D chain, mitochondrial (ATP5H) / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / Mitochondrial ATPase inhibitor, IATP / ATP synthase gamma subunit signature. / ATP synthase alpha/beta family, beta-barrel domain / F1F0 ATP synthase subunit C superfamily / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase alpha/beta chain, C terminal domain / ATP synthase / ATP synthase delta (OSCP) subunit / ATP synthase subunit C / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase c subunit signature. / ATP synthase alpha/beta family, nucleotide-binding domain / mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase, catalytic core / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / angiostatin binding / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / negative regulation of hydrolase activity / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transporter activity / proton-transporting ATPase activity, rotational mechanism / ATP hydrolysis coupled proton transport / negative regulation of endothelial cell proliferation / H+-transporting two-sector ATPase / heme biosynthetic process / ATP synthesis coupled proton transport / mitochondrial nucleoid / negative regulation of ATPase activity / mitochondrial membrane / erythrocyte differentiation / ATPase binding / mitochondrial inner membrane / protein homotetramerization / protein homooligomerization / calmodulin binding / lipid binding / cell surface / mitochondrion / protein homodimerization activity / integral component of membrane / ATP binding / ATP synthase subunit 4, mitochondrial / ATP synthase subunit 5, mitochondrial / F0F1-type ATP synthase, epsilon subunit (Mitochondrial delta subunit) / ATP synthase subunit beta / ATP synthase subunit a / ATP synthase subunit d, mitochondrial / ATP synthase subunit alpha / ATPase inhibitor, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit gamma
Function and homology information
Specimen sourceBos taurus (cattle)
Ogataea angusta (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.8 Å resolution
AuthorsVinothkumar, K.R. / Montgomery, M.G. / Liu, S. / Walker, J.E.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.
Authors: 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 1234ABCDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein/peptide ATP synthase subunit f /


Mass: 2571.161 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#2: Protein/peptide ATP synthase subunit AAP1 /


Mass: 2145.636 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#3: Protein/peptide ATP synthase subunit a /


Mass: 1464.797 Da / Num. of mol.: 1 / Details: Helix 1 of subunit a / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#4: Protein/peptide ATP synthase subunit b /


Mass: 2315.846 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#5: Protein/peptide ATP synthase alpha subunit


Mass: 55007.535 Da / Num. of mol.: 3 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: W1Q6W1*PLUS
#6: Protein/peptide ATP synthase beta subunit


Mass: 50852.434 Da / Num. of mol.: 3 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: W1QA59*PLUS
#7: Protein/peptide ATP synthase gamma subunit /


Mass: 29418.238 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: W1QGS3*PLUS
#8: Protein/peptide ATP synthase delta subunit /


Mass: 14171.783 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: W1QBD1*PLUS
#9: Protein/peptide ATP synthase epsilon subunit


Mass: 6910.886 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#10: Protein/peptide ATP synthase inhibitor protein IF1


Mass: 7462.098 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P01096*PLUS
#11: Protein/peptide
ATP synthase c subunit


Mass: 7837.380 Da / Num. of mol.: 10 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: E7E832*PLUS
#12: Protein/peptide ATP synthase OSCP subunit


Mass: 20678.812 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: W1QCI5*PLUS
#13: Protein/peptide ATP synthase subunit b /


Mass: 22292.332 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: W1Q9V2*PLUS
#14: Protein/peptide ATP synthase subunit d /


Mass: 16427.818 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: W1Q731*PLUS
#15: Protein/peptide ATP synthase subunit h /


Mass: 1805.216 Da / Num. of mol.: 1 / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#16: Protein/peptide ATP synthase subunit a /


Mass: 27559.775 Da / Num. of mol.: 1 / Details: helices 4, 5 and 6 / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: E7E837*PLUS
#17: Protein/peptide ATP synthase subunit a /


Mass: 3762.629 Da / Num. of mol.: 1 / Details: Helices 2 and 3 of subunit a / Source: (natural) Ogataea angusta (fungus) / Variant: A16

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Non-polymers , 3 types, 11 molecules

#18: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#19: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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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 MDa
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
22870730Ogataea angusta (fungus)
339913Bos taurus (cattle)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer ID
120 mMTris-HCL1
2100 mMsodium chloride1
32 mMMagnesium sulphate1
42 mMATP1
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 FIELDBright-field microscopy / 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 / Width: 4096 / Height: 4096 / Movie frames/image: 69 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategoryDetails
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.
2EPUimage acquisitionOne image was collected for each hole
4CTFFIND3CTF correctionCTF correction was applied to each particle in RELION
7Coot0.8.3model fitting
12RELION1.4classification
13RELION1.43D reconstruction
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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