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- EMDB-21238: Chloroplast ATP synthase (C2, CF1FO) -

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Basic information

Entry
Database: EMDB / ID: EMD-21238
TitleChloroplast ATP synthase (C2, CF1FO)
Map dataC2, CF1FO
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 subunit b, chloroplastic
    • Protein or peptide: ATP synthase subunit b', chloroplastic
    • Protein or peptide: ATP synthase subunit a, 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
    • Protein or peptide: ATP synthase subunit c, chloroplastic
KeywordsCF1FO / ATP synthase / PHOTOSYNTHESIS / PHOTOSYNTHESIS-TRANSLOCASE complex
Function / homology
Function and homology information


: / chloroplast thylakoid membrane / proton-transporting ATP synthase complex, coupling factor F(o) / 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 ...: / chloroplast thylakoid membrane / proton-transporting ATP synthase complex, coupling factor F(o) / 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 / ADP binding / lipid binding / ATP hydrolysis activity / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.08 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 27, 2020-
Header (metadata) releaseFeb 26, 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: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vm4
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21238.png

Downloads & links

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Map

FileDownload / File: emd_21238.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC2, CF1FO
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 288 pix.
= 339.84 Å		1.18 Å/pix.
x 288 pix.
= 339.84 Å		1.18 Å/pix.
x 288 pix.
= 339.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.012
Minimum - Maximum-0.008705234 - 0.031148724
Average (Standard dev.)0.00030832988 (±0.0018054285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 339.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.181.181.18
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z339.840339.840339.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0090.0310.000

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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 subunit b, chloroplastic
    • Protein or peptide: ATP synthase subunit b', chloroplastic
    • Protein or peptide: ATP synthase subunit a, 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
    • Protein or peptide: ATP synthase subunit c, chloroplastic

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Supramolecule #1: Chloroplast ATP synthase

SupramoleculeName: Chloroplast ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Control rotary state 2
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 subunit b, chloroplastic

MacromoleculeName: ATP synthase subunit b, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 21.013904 KDa
SequenceString:
MKNVTDSFVF LGHWPSAGSF GFNTDILATN LINLSVVLGV LIFFGKGVLS DLLDNRKQRI LNTIRNSEEL RGKAIEQLEK ARARLKKVE MDADQFRVNG YSEIEREKMN LINSTYKTLE QFENYKNETI QFEQQKAINQ VRQRVFQQAL QGALGTLNSC L NNELHLRT INANIGMFGA MNEITD

UniProtKB: ATP synthase subunit b, chloroplastic

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Macromolecule #4: ATP synthase subunit b', chloroplastic

MacromoleculeName: ATP synthase subunit b', chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 24.487596 KDa
SequenceString: MANMLVASSS KTLPTTTTTT ITPKPKFPLL KTPLLKLSPP QLPPLKHLNL SVLKSAAITA TPLTLSFLLP YPSLAEEIEK ASLFDFNLT LPIIMAEFLF LMFALDKIYY TPLGDFMDKR DASIKEQLSG VKDTSSEVKQ LEEQANAVMR AARAEISAAL N KMKKETQL ...String:
MANMLVASSS KTLPTTTTTT ITPKPKFPLL KTPLLKLSPP QLPPLKHLNL SVLKSAAITA TPLTLSFLLP YPSLAEEIEK ASLFDFNLT LPIIMAEFLF LMFALDKIYY TPLGDFMDKR DASIKEQLSG VKDTSSEVKQ LEEQANAVMR AARAEISAAL N KMKKETQL EVEAKLAEGR KKIEVELQEA LGSLEQQKED TIKSLDSQIS ALSDDIVKKV LPVS

UniProtKB: ATP synthase subunit b', chloroplastic

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Macromolecule #5: ATP synthase subunit a, chloroplastic

MacromoleculeName: ATP synthase subunit a, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.10268 KDa
SequenceString: MNVLSYSINP LKGLYAISGV EVGQHFYWQI GGFQIHGQVL ITSWVVIAIL LGSAAIAVRS PQTIPTGGQN FFEYVLEFIR DVSKTQIGE EYRPWVPFIG TMFLFIFVSN WSGALLPWKI IQLPHGELAA PTNDINTTVA LALLTSVAYF YAGLTKKGLG Y FGKYIQPT ...String:
MNVLSYSINP LKGLYAISGV EVGQHFYWQI GGFQIHGQVL ITSWVVIAIL LGSAAIAVRS PQTIPTGGQN FFEYVLEFIR DVSKTQIGE EYRPWVPFIG TMFLFIFVSN WSGALLPWKI IQLPHGELAA PTNDINTTVA LALLTSVAYF YAGLTKKGLG Y FGKYIQPT PILLPINILE DFTKPLSLSF RLFGNILADE LVVVVLVSLV PLVVPIPVMF LGLFTSGIQA LIFATLAAAY IG ESLEGHH

UniProtKB: ATP synthase subunit a, chloroplastic

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Macromolecule #6: ATP synthase delta chain, chloroplastic

MacromoleculeName: ATP synthase delta chain, chloroplastic / type: protein_or_peptide / ID: 6 / 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 #7: ATP synthase epsilon chain, chloroplastic

MacromoleculeName: ATP synthase epsilon chain, chloroplastic / type: protein_or_peptide / ID: 7 / 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 #8: ATP synthase gamma chain, chloroplastic

MacromoleculeName: ATP synthase gamma chain, chloroplastic / type: protein_or_peptide / ID: 8 / 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 #9: ATP synthase subunit c, chloroplastic

MacromoleculeName: ATP synthase subunit c, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 7.977366 KDa
SequenceString:
MNPLIAAASV IAAGLAVGLA SIGPGVGQGT AAGQAVEGIA RQPEAEGKIR GTLLLSLAFM EALTIYGLVV ALALLFANPF V

UniProtKB: ATP synthase subunit c, chloroplastic

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 43.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 48077 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.4) / Number images used: 26291
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.4)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-6vm4:
Chloroplast ATP synthase (C2, CF1FO)

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