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

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Basic information

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
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / ATPase inhibitor activity / negative regulation of hydrolase activity / : / : / heme biosynthetic process / : / : / : ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / ATPase inhibitor activity / negative regulation of hydrolase activity / : / : / heme biosynthetic process / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / 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 / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
: / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial ...: / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 4, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit a ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 4, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit a / ATPase inhibitor, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit 5, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
Ogataea angusta (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å
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 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
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 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 31, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Sep 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 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 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
Polymers554,94130
Non-polymers2,76511
Water00
1


  • Idetical with deposited unit
  • defined by author
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: C0HK51*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: C0HK52*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: C0HK53*PLUS
#8: Protein ATP synthase delta 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 / References: UniProt: A0A1L1QK34*PLUS
#10: Protein ATP synthase inhibitor protein IF1


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


Mass: 7837.380 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Ogataea angusta (fungus) / Variant: A16 / References: UniProt: C0HK59*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: C0HK58*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: C0HK60*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 / 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


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


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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Yeast F1FO ATP SynthaseCOMPLEXThe complex comprises of the catalytic domain, membrane domain and peripheral stalk of the yeast ATP synthase.#1-#170MULTIPLE SOURCES
2Yeast F1FO ATP SynthaseCOMPLEXYeast F1FO ATP Synthase#1-#9, #11-#171NATURAL
3ATP synthase inhibitor protein IF1COMPLEXATP synthase inhibitor protein IF1#101RECOMBINANT
Molecular weightValue: 0.55 MDa
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Ogataea angusta (fungus)870730
33Bos taurus (cattle)9913
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 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The enzyme with bound inhibitor protein extracted in DDM 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 FIELD / 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 / Specimen holder 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 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 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: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23065 / Num. of class averages: 2 / 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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