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- PDB-5lqz: Structure of F-ATPase from Pichia angusta, state1 -

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Entry
Database: PDB / ID: 5lqz
TitleStructure of F-ATPase from Pichia angusta, state1
Components(ATP synthase ...) x 17
KeywordsHYDROLASE / ATP synthase
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, central stalk / angiostatin binding / mitochondrial proton-transporting ATP synthase, stator stalk / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial nucleoid / mitochondrial ATP synthesis coupled proton transport / heme biosynthetic process ...mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, central stalk / angiostatin binding / mitochondrial proton-transporting ATP synthase, stator stalk / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial nucleoid / mitochondrial ATP synthesis coupled proton transport / heme biosynthetic process / negative regulation of endothelial cell proliferation / negative regulation of ATPase activity / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / ATP synthesis coupled proton transport / proton transmembrane transporter activity / H+-transporting two-sector ATPase / negative regulation of hydrolase activity / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / mitochondrial membrane / ADP binding / mitochondrial inner membrane / protein homotetramerization / ATPase binding / calmodulin binding / lipid binding / ATPase / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / membrane / integral component of membrane / ATP binding / identical protein binding
ATP synthase A chain / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase, F0 complex, subunit B / ATP synthase, F0 complex, subunit B/MI25 ...ATP synthase A chain / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase, F0 complex, subunit B / ATP synthase, F0 complex, subunit B/MI25 / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / Mitochondrial ATPase inhibitor / ATP synthase, F1 complex, beta subunit / ATP synthase, F1 complex, alpha subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / AAA+ ATPase domain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, alpha subunit, C-terminal / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / P-loop containing nucleoside triphosphate hydrolase / ATP synthase, F0 complex, subunit A / ATP synthase alpha/beta family, nucleotide-binding domain / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase delta (OSCP) subunit / ATP synthase subunit C / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase / ATP synthase alpha/beta family, beta-barrel domain / ATP synthase alpha/beta chain, C terminal domain / F1F0 ATP synthase subunit C superfamily / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal domain superfamily / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit superfamily / F/V-ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit A superfamily / ATPase, OSCP/delta subunit / V-ATPase proteolipid subunit C-like domain / ATP synthase, F0 complex, subunit C / ATP synthase, F1 complex, gamma subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
ATP synthase subunit d, mitochondrial / ATP synthase subunit 4, mitochondrial / ATP synthase subunit beta / ATP synthase subunit delta, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit gamma / ATP synthase subunit alpha / ATP synthase subunit a / ATP synthase subunit 9, mitochondrial / ATPase inhibitor, mitochondrial
Biological speciesOgataea angusta (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsVinothkumar, K.R. / Montgomery, M.G. / Liu, S. / Walker, J.E.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (United Kingdom)MC_U105663150 United Kingdom
Medical Research Council (United Kingdom)MC_U105184322 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Experimental preparation / Category: em_sample_support / em_software / Item: _em_sample_support.grid_type / _em_software.name
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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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 subunit c
L: ATP synthase subunit c
M: ATP synthase subunit c
N: ATP synthase subunit c
O: ATP synthase subunit c
P: ATP synthase subunit c
Q: ATP synthase subunit c
R: ATP synthase subunit c
S: ATP synthase subunit c
T: ATP synthase subunit c
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
Polymers554,94130
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 method: isolated from a natural source / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#2: Protein/peptide ATP synthase subunit AAP1 /


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


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 method: isolated from a natural source / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#5: Protein ATP synthase alpha subunit


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


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


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


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


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


Mass: 7462.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: P01096*PLUS
#11: Protein
ATP synthase subunit c /


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


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


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


Mass: 16427.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 method: isolated from a natural source / Source: (natural) Ogataea angusta (fungus) / Variant: A16
#16: Protein ATP synthase subunit a /


Mass: 27559.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Helices 4, 5 and 6 of subunit a / 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 / Source method: isolated from a natural source / 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 / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#19: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#20: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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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-#17 / Source: NATURAL
Molecular weightValue: 0.55 MDa / Experimental value: NO
Source (natural)Organism: Ogataea angusta (fungus) / Strain: A16
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMTris-HClTris1
2100 mMsodium chloride1
32 mMMagnesium sulphate1
41 mMATPAdenosine triphosphate1
50.05 %Cymal-71
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The enzyme with bound inhibitor protein extracted and purified in Cymal-7.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
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
MicroscopyModel: 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 X / Calibrated magnification: 81395 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 87.5 K
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 µm / 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 was corrected per particle in RELION
7Coot0.8.3model fitting
11RELION1.4classification
12RELION1.43D 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 correctionDetails: CTF was estimated using the whole micrograph using all the frames. CTF was corrected per particle in RELION.
Type: NONE
Particle selectionNum. of particles selected: 123683
Details: 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.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42771 / Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
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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