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- EMDB-21267: Chloroplast ATP synthase (R3, CF1) -

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Basic information

Entry
Database: EMDB / ID: EMD-21267
TitleChloroplast ATP synthase (R3, CF1)
Map dataR3, F1
Sample
  • Complex: Chloroplast ATP synthase
    • Protein or peptide: ATP synthase subunit alpha, chloroplastic
    • Protein or peptide: ATP synthase subunit beta, chloroplastic
    • Protein or peptide: ATP synthase delta chain, chloroplastic
    • Protein or peptide: ATP synthase epsilon chain, chloroplastic
    • Protein or peptide: ATP synthase gamma chain, chloroplastic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: TENTOXIN
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCF1FO / ATP synthase / PHOTOSYNTHESIS / TRANSLOCASE
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven 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 / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsYang J-H / Williams D
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, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-6vok
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21267.png

Downloads & links

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Map

FileDownload / File: emd_21267.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationR3, F1
Voxel sizeX=Y=Z: 1.053 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.01
Minimum - Maximum-0.05592174 - 0.0932672
Average (Standard dev.)0.00005337321 (±0.0014157691)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 442.25998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0531.0531.053
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z442.260442.260442.260
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0560.0930.000

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Supplemental data

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Sample components

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Entire : Chloroplast ATP synthase

EntireName: Chloroplast ATP synthase
Components
  • Complex: Chloroplast ATP synthase
    • Protein or peptide: ATP synthase subunit alpha, chloroplastic
    • Protein or peptide: ATP synthase subunit beta, chloroplastic
    • Protein or peptide: ATP synthase delta chain, chloroplastic
    • Protein or peptide: ATP synthase epsilon chain, chloroplastic
    • Protein or peptide: ATP synthase gamma chain, chloroplastic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: TENTOXIN
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Chloroplast ATP synthase

SupramoleculeName: Chloroplast ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: Reduced rotary state 3 (CF1)
Source (natural)Organism: Spinacia oleracea (spinach) / Tissue: Leaves
Molecular weightTheoretical: 594.35 KDa

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Macromolecule #1: ATP synthase subunit alpha, chloroplastic

MacromoleculeName: ATP synthase subunit alpha, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 55.505199 KDa
SequenceString: MATIRADEIS KIIRERIEGY NREVKVVNTG TVLQVGDGIA RIHGLDEVMA GELVEFEEGT IGIALNLESN NVGVVLMGDG LMIQEGSSV KATGRIAQIP VSEAYLGRVI NALAKPIDGR GEITASESRL IESPAPGIMS RRSVYEPLQT GLIAIDAMIP V GRGQRELI ...String:
MATIRADEIS KIIRERIEGY NREVKVVNTG TVLQVGDGIA RIHGLDEVMA GELVEFEEGT IGIALNLESN NVGVVLMGDG LMIQEGSSV KATGRIAQIP VSEAYLGRVI NALAKPIDGR GEITASESRL IESPAPGIMS RRSVYEPLQT GLIAIDAMIP V GRGQRELI IGDRQTGKTA VATDTILNQQ GQNVICVYVA IGQKASSVAQ VVTNFQERGA MEYTIVVAET ADSPATLQYL AP YTGAALA EYFMYRERHT LIIYDDLSKQ AQAYRQMSLL LRRPPGREAY PGDVFYLHSR LLERAAKLSS LLGEGSMTAL PIV ETQAGD VSAYIPTNVI SITDGQIFLS ADLFNAGIRP AINVGISVSR VGSAAQIKAM KKVAGKLKLE LAQFAELEAF AQFA SDLDK ATQNQLARGQ RLRELLKQPQ SAPLTVEEQV MTIYTGTNGY LDSLELDQVR KYLVELRTYV KTNKPEFQEI ISSTK TFTE EAEALLKEAI QEQMERFLLQ EQA

UniProtKB: ATP synthase subunit alpha, chloroplastic

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Macromolecule #2: ATP synthase subunit beta, chloroplastic

MacromoleculeName: ATP synthase subunit beta, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 53.797367 KDa
SequenceString: MRINPTTSDP GVSTLEKKNL GRIAQIIGPV LDVAFPPGKM PNIYNALIVK GRDTAGQPMN VTCEVQQLLG NNRVRAVAMS ATDGLTRGM EVIDTGAPLS VPVGGATLGR IFNVLGEPVD NLGPVDTRTT SPIHRSAPAF TQLDTKLSIF ETGIKVVDLL A PYRRGGKI ...String:
MRINPTTSDP GVSTLEKKNL GRIAQIIGPV LDVAFPPGKM PNIYNALIVK GRDTAGQPMN VTCEVQQLLG NNRVRAVAMS ATDGLTRGM EVIDTGAPLS VPVGGATLGR IFNVLGEPVD NLGPVDTRTT SPIHRSAPAF TQLDTKLSIF ETGIKVVDLL A PYRRGGKI GLFGGAGVGK TVLIMELINN IAKAHGGVSV FGGVGERTRE GNDLYMEMKE SGVINEQNIA ESKVALVYGQ MN EPPGARM RVGLTALTMA EYFRDVNEQD VLLFIDNIFR FVQAGSEVSA LLGRMPSAVG YQPTLSTEMG SLQERITSTK EGS ITSIQA VYVPADDLTD PAPATTFAHL DATTVLSRGL AAKGIYPAVD PLDSTSTMLQ PRIVGEEHYE IAQRVKETLQ RYKE LQDII AILGLDELSE EDRLTVARAR KIERFLSQPF FVAEVFTGSP GKYVGLAETI RGFQLILSGE LDSLPEQAFY LVGNI DEAT AKAMNLEMES KLKK

UniProtKB: ATP synthase subunit beta, chloroplastic

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Macromolecule #3: ATP synthase delta chain, chloroplastic

MacromoleculeName: ATP synthase delta chain, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.708582 KDa
SequenceString: MAALQNPVAL QSRTTTAVAA LSTSSTTSTP KPFSLSFSSS TATFNPLRLK ILTASKLTAK PRGGALGTRM VDSTASRYAS ALADVADVT GTLEATNSDV EKLIRIFSEE PVYYFFANPV ISIDNKRSVL DEIITTSGLQ PHTANFINIL IDSERINLVK E ILNEFEDV ...String:
MAALQNPVAL QSRTTTAVAA LSTSSTTSTP KPFSLSFSSS TATFNPLRLK ILTASKLTAK PRGGALGTRM VDSTASRYAS ALADVADVT GTLEATNSDV EKLIRIFSEE PVYYFFANPV ISIDNKRSVL DEIITTSGLQ PHTANFINIL IDSERINLVK E ILNEFEDV FNKITGTEVA VVTSVVKLEN DHLAQIAKGV QKITGAKNVR IKTVIDPSLV AGFTIRYGNE GSKLVDMSVK KQ LEEIAAQ LEMDDVTLAV

UniProtKB: ATP synthase delta chain, chloroplastic

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Macromolecule #4: ATP synthase epsilon chain, chloroplastic

MacromoleculeName: ATP synthase epsilon chain, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.715707 KDa
SequenceString:
MTLNLCVLTP NRSIWNSEVK EIILSTNSGQ IGVLPNHAPT ATAVDIGILR IRLNDQWLTL ALMGGFARIG NNEITILVND AERGSDIDP QEAQQTLEIA EANLRKAEGK RQKIEANLAL RRARTRVEAS NTISS

UniProtKB: ATP synthase epsilon chain, chloroplastic

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Macromolecule #5: ATP synthase gamma chain, chloroplastic

MacromoleculeName: ATP synthase gamma chain, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 40.119066 KDa
SequenceString: MACSLSFSSS VSTFHLPTTT QSTQAPPNNA TTLPTTNPIQ CANLRELRDR IGSVKNTQKI TEAMKLVAAA KVRRAQEAVV NGRPFSETL VEVLYNMNEQ LQTEDVDVPL TKIRTVKKVA LMVVTGDRGL CGGFNNMLLK KAESRIAELK KLGVDYTIIS I GKKGNTYF ...String:
MACSLSFSSS VSTFHLPTTT QSTQAPPNNA TTLPTTNPIQ CANLRELRDR IGSVKNTQKI TEAMKLVAAA KVRRAQEAVV NGRPFSETL VEVLYNMNEQ LQTEDVDVPL TKIRTVKKVA LMVVTGDRGL CGGFNNMLLK KAESRIAELK KLGVDYTIIS I GKKGNTYF IRRPEIPVDR YFDGTNLPTA KEAQAIADDV FSLFVSEEVD KVEMLYTKFV SLVKSDPVIH TLLPLSPKGE IC DINGKCV DAAEDELFRL TTKEGKLTVE RDMIKTETPA FSPILEFEQD PAQILDALLP LYLNSQILRA LQESLASELA ARM TAMSNA TDNANELKKT LSINYNRARQ AKITGEILEI VAGANACV

UniProtKB: ATP synthase gamma chain, chloroplastic

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #7: TENTOXIN

MacromoleculeName: TENTOXIN / type: ligand / ID: 7 / Number of copies: 1 / Formula: TTX
Molecular weightTheoretical: 414.498 Da
Chemical component information

ChemComp-TTX:
TENTOXIN / toxin*YM / Tentoxin

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.8000000000000003 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta-commit-da823c)
Final 3D classificationSoftware - Name: RELION (ver. 3.1-beta-commit-da823c)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta-commit-da823c)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1-beta-commit-da823c) / Number images used: 10264
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fki


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6vok:
Chloroplast ATP synthase (R3, CF1)

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