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- PDB-6vol: Chloroplast ATP synthase (R2, CF1FO) -

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Basic information

Entry
Database: PDB / ID: 6vol
TitleChloroplast ATP synthase (R2, CF1FO)
Components(ATP synthase ...) x 9
KeywordsTRANSLOCASE / PHOTOSYNTHESIS / CF1FO / ATP synthase
Function / homology
Function and homology information


photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / proton motive force-driven ATP synthesis / : / proton motive force-driven mitochondrial ATP synthesis / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism ...photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / proton motive force-driven ATP synthesis / : / proton motive force-driven mitochondrial ATP synthesis / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit b' / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. ...ATP synthase, F0 complex, subunit b' / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / 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 / TENTOXIN / ATP synthase subunit beta, chloroplastic / ATP synthase epsilon chain, chloroplastic / ATP synthase gamma chain, chloroplastic / ATP synthase subunit alpha, chloroplastic / ATP synthase subunit a, chloroplastic / ATP synthase subunit b, chloroplastic / ATP synthase delta chain, chloroplastic ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / TENTOXIN / ATP synthase subunit beta, chloroplastic / ATP synthase epsilon chain, chloroplastic / ATP synthase gamma chain, chloroplastic / ATP synthase subunit alpha, chloroplastic / ATP synthase subunit a, chloroplastic / ATP synthase subunit b, chloroplastic / ATP synthase delta chain, chloroplastic / ATP synthase subunit b', chloroplastic / ATP synthase subunit c, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsYang, J.-H. / Williams, D. / Kandiah, E. / Fromme, P. / Chiu, P.-L.
CitationJournal: Commun Biol / Year: 2020
Title: Structural basis of redox modulation on chloroplast ATP synthase.
Authors: Jay-How Yang / Dewight Williams / Eaazhisai Kandiah / Petra Fromme / Po-Lin Chiu /
Abstract: In higher plants, chloroplast ATP synthase has a unique redox switch on its γ subunit that modulates enzyme activity to limit ATP hydrolysis at night. To understand the molecular details of the ...In higher plants, chloroplast ATP synthase has a unique redox switch on its γ subunit that modulates enzyme activity to limit ATP hydrolysis at night. To understand the molecular details of the redox modulation, we used single-particle cryo-EM to determine the structures of spinach chloroplast ATP synthase in both reduced and oxidized states. The disulfide linkage of the oxidized γ subunit introduces a torsional constraint to stabilize the two β hairpin structures. Once reduced, free cysteines alleviate this constraint, resulting in a concerted motion of the enzyme complex and a smooth transition between rotary states to facilitate the ATP synthesis. We added an uncompetitive inhibitor, tentoxin, in the reduced sample to limit the flexibility of the enzyme and obtained high-resolution details. Our cryo-EM structures provide mechanistic insight into the redox modulation of the energy regulation activity of chloroplast ATP synthase.
History
DepositionJan 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: ATP synthase subunit alpha, chloroplastic
B: ATP synthase subunit alpha, chloroplastic
C: ATP synthase subunit alpha, chloroplastic
D: ATP synthase subunit beta, chloroplastic
E: ATP synthase subunit beta, chloroplastic
F: ATP synthase subunit beta, chloroplastic
d: ATP synthase delta chain, chloroplastic
g: ATP synthase gamma chain, chloroplastic
e: ATP synthase epsilon chain, chloroplastic
I: ATP synthase subunit b, chloroplastic
J: ATP synthase subunit b', chloroplastic
a: ATP synthase subunit a, chloroplastic
M: ATP synthase subunit c, chloroplastic
N: ATP synthase subunit c, chloroplastic
O: ATP synthase subunit c, chloroplastic
P: ATP synthase subunit c, chloroplastic
Q: ATP synthase subunit c, chloroplastic
R: ATP synthase subunit c, chloroplastic
S: ATP synthase subunit c, chloroplastic
T: ATP synthase subunit c, chloroplastic
U: ATP synthase subunit c, chloroplastic
V: ATP synthase subunit c, chloroplastic
W: ATP synthase subunit c, chloroplastic
X: ATP synthase subunit c, chloroplastic
Y: ATP synthase subunit c, chloroplastic
Z: ATP synthase subunit c, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)598,03633
Polymers594,73826
Non-polymers3,2987
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 9 types, 26 molecules ABCDEFdgeIJaMNOPQRSTUVWXYZ

#1: Protein ATP synthase subunit alpha, chloroplastic / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55505.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P06450, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta, chloroplastic / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 53797.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P00825, H+-transporting two-sector ATPase
#3: Protein ATP synthase delta chain, chloroplastic / F-ATPase delta chain


Mass: 27708.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P11402
#4: Protein ATP synthase gamma chain, chloroplastic / F-ATPase gamma subunit


Mass: 40119.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P05435
#5: Protein ATP synthase epsilon chain, chloroplastic / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14715.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P00833
#6: Protein ATP synthase subunit b, chloroplastic / ATP synthase F(0) sector subunit b / ATPase subunit I


Mass: 21013.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06453
#7: Protein ATP synthase subunit b', chloroplastic / ATP synthase F(0) sector subunit b' / ATPase subunit II


Mass: 24487.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P31853
#8: Protein ATP synthase subunit a, chloroplastic / ATP synthase F0 sector subunit a / F-ATPase subunit IV


Mass: 27102.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06451
#9: Protein
ATP synthase subunit c, chloroplastic / ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase ...ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 7977.366 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69447

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Non-polymers , 3 types, 7 molecules

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


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#12: Chemical ChemComp-TTX / TENTOXIN


Mass: 414.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N4O4 / Comment: toxin*YM

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Details

Has ligand of interestN

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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: Chloroplast ATP synthase / Type: COMPLEX / Details: Reduced rotary state 2 (CF1FO) / Entity ID: #1-#9 / Source: NATURAL
Molecular weightValue: 0.59435 MDa / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach) / Tissue: Leaves
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/2 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 130000 X / Nominal defocus max: -2800 nm / Nominal defocus min: -1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 43.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansSampling size: 5 µm

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.16_3546refinement
PHENIX1.16_3546refinement
EM software
IDNameVersionCategory
2EPU1.11image acquisition
4CTFFIND4.1.13CTF correction
7Coot0.9-premodel fitting
9RELION3.1-beta-commit-da823cinitial Euler assignment
10RELION3.1-beta-commit-da823cfinal Euler assignment
11RELION3.1-beta-commit-da823cclassification
12RELION3.1-beta-commit-da823c3D reconstruction
13PHENIX1.17_3644model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29667 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6FKH

6fkh


Accession code: 6FKH / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 33.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00539537
ELECTRON MICROSCOPYf_angle_d0.845853623
ELECTRON MICROSCOPYf_chiral_restr0.04676417
ELECTRON MICROSCOPYf_plane_restr0.01116914
ELECTRON MICROSCOPYf_dihedral_angle_d15.038224004

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