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- PDB-6vmd: Chloroplast ATP synthase (C1, CF1) -

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Basic information

Entry
Database: PDB / ID: 6vmd
TitleChloroplast ATP synthase (C1, CF1)
Components(ATP synthase ...) x 5
KeywordsPHOTOSYNTHESIS/TRANSLOCASE / CF1FO / ATP synthase / PHOTOSYNTHESIS / PHOTOSYNTHESIS-TRANSLOCASE complex
Function / homology
Function and homology information


: / chloroplast thylakoid membrane / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / 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 / ADP binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / 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 subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / 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, 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 / 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 beta, chloroplastic / ATP synthase epsilon chain, chloroplastic / ATP synthase gamma chain, chloroplastic / ATP synthase subunit alpha, chloroplastic / ATP synthase delta chain, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.53 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 27, 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

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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
e: ATP synthase epsilon chain, chloroplastic
g: ATP synthase gamma chain, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,90714
Polymers410,4519
Non-polymers2,4565
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 ... , 5 types, 9 molecules ABCDEFdeg

#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 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
#5: 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

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Non-polymers , 2 types, 5 molecules

#6: 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
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*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: Control rotary state 3 / Entity ID: #1-#5 / 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
VitrificationCryogen 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: 22500 X / Calibrated magnification: 48077 X / Nominal defocus max: -4000 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: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
2SerialEM4.8.6image acquisition
4CTFFIND4.1.13CTF correction
7Coot0.9-premodel fitting
9RELION3.0.4initial Euler assignment
10RELION3.0.4final Euler assignment
11RELION3.0.4classification
12RELION3.0.43D reconstruction
13PHENIX1.17_3644model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127760 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 129.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007727883
ELECTRON MICROSCOPYf_angle_d1.062137786
ELECTRON MICROSCOPYf_chiral_restr0.05974447
ELECTRON MICROSCOPYf_plane_restr0.00724912
ELECTRON MICROSCOPYf_dihedral_angle_d20.93473939

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