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- EMDB-68717: Cryo-EM structure of Chlamydomonas reinhardtii chloroplast F1Fo-A... -

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Basic information

Entry
Database: EMDB / ID: EMD-68717
TitleCryo-EM structure of Chlamydomonas reinhardtii chloroplast F1Fo-ATP synthase
Map data
Sample
  • Complex: F1Fo-ATP synthase
    • Protein or peptide: x 9 types
  • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsChlamydomonas reinhardtii / chloroplast / F1Fo-ATP synthase / ELECTRON TRANSPORT
Function / homology
Function and homology information


proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding ...proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / 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, alpha subunit nucleotide-binding domain / 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 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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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 b', chloroplastic / ATP synthase subunit a, chloroplastic / ATP synthase subunit beta, chloroplastic / ATP synthase epsilon chain, chloroplastic / ATP synthase gamma chain, chloroplastic / ATP synthase subunit alpha, chloroplastic / ATP synthase subunit c, chloroplastic / ATP synthase delta chain, chloroplastic / ATP synthase subunit b, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu J / Li DY / Guan ZY / Yin P / Yan JJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Cryo-EM structure of Chlamydomonas reinhardtii chloroplast FF-ATP synthase.
Authors: Jian Liu / Danyang Li / Qiang Wang / Ping Yin / Zeyuan Guan / Junjie Yan /
Abstract: FF-ATP synthase is a multi-subunit energy-producing macromolecular machine, consisting of hydrophilic F and hydrophobic F segments, which utilize transmembrane electrochemical potential to synthesize ...FF-ATP synthase is a multi-subunit energy-producing macromolecular machine, consisting of hydrophilic F and hydrophobic F segments, which utilize transmembrane electrochemical potential to synthesize ATP from ADP and inorganic phosphate. ATP synthases are widely distributed in the inner membrane of mitochondria, the thylakoid membrane of chloroplasts, and the plasma membrane of bacteria. To date, a comprehensively structural study on chloroplast FF-ATP synthase is very limited compared with their counterparts in mitochondria and bacteria. In this study, we in-situ extracted and purified chloroplast FF-ATP synthase from the photosynthetic unicellular green algae Chlamydomonas reinhardtii. The ATPase activity of the holoenzyme was validated by a combination of BN-PAGE separation and in-gel detection. We determined the structure of Chlamydomonas reinhardtii FF-ATP synthase at 3.2 Å resolution using single particle cryo-electron microscopy (cryo-EM). The structure is in an oxidized state with a disulfide bond formation in the γ subunit. More acidic residues were found to be involved in the proton translocation across the F segment compared with their counterparts of the higher plants. Overall, the structure presented here provides novel structural information, giving us comprehensive understanding of the photosynthetic chloroplast FF-ATP synthase from lower unicellular algae to higher plants.
History
DepositionJan 25, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68717.png

Downloads & links

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Map

FileDownload / File: emd_68717.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.6828829 - 1.4175221
Average (Standard dev.)0.001813732 (±0.04724138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68717_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_68717_half_map_2.map
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Sample components

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Entire : F1Fo-ATP synthase

EntireName: F1Fo-ATP synthase
Components
  • Complex: F1Fo-ATP synthase
    • Protein or peptide: ATP synthase subunit alpha, chloroplastic
    • Protein or peptide: ATP synthase subunit a, chloroplastic
    • Protein or peptide: ATP synthase subunit b', chloroplastic
    • Protein or peptide: ATP synthase gamma chain, chloroplastic
    • Protein or peptide: ATP synthase subunit beta, chloroplastic
    • Protein or peptide: ATP synthase delta chain, chloroplastic
    • Protein or peptide: ATP synthase subunit b, chloroplastic
    • Protein or peptide: ATP synthase epsilon chain, chloroplastic
    • Protein or peptide: ATP synthase subunit c, chloroplastic
  • Protein or peptide: ATP synthase subunit alpha, chloroplastic
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: F1Fo-ATP synthase

SupramoleculeName: F1Fo-ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #8, #1-#3, #10, #4-#7
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: ATP synthase subunit a, chloroplastic

MacromoleculeName: ATP synthase subunit a, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 24.538498 KDa
SequenceString: VGQHYYWELG GYELHGQVLI TSWVVLGILA VLSFLGNTNL KSTPDGFQNF TELVTEFIRD LAKTQIGEED YLKWVPFLGT IFLFIFVSN WSGALLPYRL IEIPNGELAA PTNDINTTVA LALLTSISYF YAGISKKGLG YFSRYVEPAA FLLPINVLED F TKPLSLSF ...String:
VGQHYYWELG GYELHGQVLI TSWVVLGILA VLSFLGNTNL KSTPDGFQNF TELVTEFIRD LAKTQIGEED YLKWVPFLGT IFLFIFVSN WSGALLPYRL IEIPNGELAA PTNDINTTVA LALLTSISYF YAGISKKGLG YFSRYVEPAA FLLPINVLED F TKPLSLSF RLFGNILADE LVVGVLVALV PLIIPIPIML LGVFTSAIQA LVFATLAGAY INEAL

UniProtKB: ATP synthase subunit a, chloroplastic

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Macromolecule #2: ATP synthase subunit b', chloroplastic

MacromoleculeName: ATP synthase subunit b', chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 14.161326 KDa
SequenceString:
VMAGEFLLLM VFLEKTWFTP VGKVLDERDN LIRSKLGSVK DNTGDVDKLV LEAETILKSA RSDVSAMINT KKAAKQSELD KTYNEAKAK ITAEVESSIA GLEQESASML KSLDAQVDKI SAEVLKRVLP

UniProtKB: ATP synthase subunit b', chloroplastic

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Macromolecule #3: ATP synthase gamma chain, chloroplastic

MacromoleculeName: ATP synthase gamma chain, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 35.283652 KDa
SequenceString: LKEVRDRIAS VKNTQKITDA MKLVAAAKVR RAQEAVVNGR PFSENLVKVL YGVNQRVRQE DVDSPLCAVR PVKSVLLVVL TGDRGLCGG YNNFIIKKTE ARYRELTAMG VKVNLVCVGR KGAQYFARRK QYNIVKSFSL GAAPSTKEAQ GIADEIFASF I AQESDKVE ...String:
LKEVRDRIAS VKNTQKITDA MKLVAAAKVR RAQEAVVNGR PFSENLVKVL YGVNQRVRQE DVDSPLCAVR PVKSVLLVVL TGDRGLCGG YNNFIIKKTE ARYRELTAMG VKVNLVCVGR KGAQYFARRK QYNIVKSFSL GAAPSTKEAQ GIADEIFASF I AQESDKVE LVFTKFISLI NSNPTIQTLL PMTPMGELCD VDGKCVDAAD DEIFKLTTKG GEFAVEREKT TIETEALDPS LI FEQEPAQ ILDALLPLYM SSCLLRSLQE ALASELAARM NAMNNASDNA KELKKGLTVQ YNKQRQAKIT QELAEIVGGA AAT SG

UniProtKB: ATP synthase gamma chain, chloroplastic

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Macromolecule #4: ATP synthase delta chain, chloroplastic

MacromoleculeName: ATP synthase delta chain, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 19.165072 KDa
SequenceString:
SESYAKALVE LADEKGKLEA VHADVDAVAG LMKENAKLSA LIMNPVVESD KKRAVLAKIA KEAGFQQYTI NWLNLLVEKD RLSLVPEIC ECFEDLYCQM TDTQVATLRS AVKLEQEQQF LIAKKLQELT GSKNIKLKPV IDSSLIAGFV VEYGSSQIDL S VRGQIERV ADQLT

UniProtKB: ATP synthase delta chain, chloroplastic

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Macromolecule #5: ATP synthase subunit b, chloroplastic

MacromoleculeName: ATP synthase subunit b, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 17.584096 KDa
SequenceString:
ETNIINLAAV VGIVVSFVGK NLSSLLEDRK NTIVKNLEEA NQRAIEAEQK LTAARTQLET AKKKAQEIRE EGVLRATQEI NNVVSQHEL RLARLQEFKQ ETLAFYQQKA FKQAYLYVIN KIMTRVRERL NKGLDSTYHV VVNNFYVSRF TQF

UniProtKB: ATP synthase subunit b, chloroplastic

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Macromolecule #6: ATP synthase epsilon chain, chloroplastic

MacromoleculeName: ATP synthase epsilon chain, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 14.807804 KDa
SequenceString:
MSLQISILTP ERPFWNGQAD EIILPTETGE MGVLKNHAPI ITGLNVGAML IRGGQASGSK DEWNSYAIMG GFALVKQNQV TILANEAVS AENINPEEAK DAFETAKANL EKAEGVKEKV EANFAYKRAK ARYQVVK

UniProtKB: ATP synthase epsilon chain, chloroplastic

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Macromolecule #7: ATP synthase subunit c, chloroplastic

MacromoleculeName: ATP synthase subunit c, chloroplastic / type: protein_or_peptide / ID: 7 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 7.793086 KDa
SequenceString:
PIVAATSVVS AGLAVGLAAI GPGMGQGTAA GYAVEGIARQ PEAEGKIRGA LLLSFAFMES LTIYGLVVAL ALLFANPFA

UniProtKB: ATP synthase subunit c, chloroplastic

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Macromolecule #8: ATP synthase subunit alpha, chloroplastic

MacromoleculeName: ATP synthase subunit alpha, chloroplastic / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 51.999223 KDa
SequenceString: KMVDFGIVFQ VGDGIARIYG LEKAMSGELL EFEDGTLGIA LNLEANNVGA VLLGDGLKIT EGSRVRCTGK IAEIPVGEAY LGRVVDGLA RPVDGKGAVQ TKDSRAIESP APGIVARRSV YEPLATGLVA VDAMIPVGRG QRELIIGDRQ TGKTAIAVDT I LNQKGKGV ...String:
KMVDFGIVFQ VGDGIARIYG LEKAMSGELL EFEDGTLGIA LNLEANNVGA VLLGDGLKIT EGSRVRCTGK IAEIPVGEAY LGRVVDGLA RPVDGKGAVQ TKDSRAIESP APGIVARRSV YEPLATGLVA VDAMIPVGRG QRELIIGDRQ TGKTAIAVDT I LNQKGKGV ICVYVAIGQK ASSVAQVLNT LKERGALDYT IIVMANANEP ATLQYLAPYT GATLAEYFMY TGRPTLTIYD DL SKQAQAY REMSLLLRRP PGREAYPGDV FYLHSRLLER AAKLNNALGE GSMTALPIVE TQEGDVSAYI PTNVISITDG QIF LAAGLF NSGLRPAINV GISVSRVGSA AQPKAMKQVA GKLKLELAQF AELEAFSQFA SDLDQATQNQ LARGARLREI LKQP QSSPL SVEEQVASLY AGTNGYLDKL EVSQVRAYLS GLRSYLANSY PKYGEILRST LTFTPEAEGL VKQAINEYLE EFKSQ AKAA

UniProtKB: ATP synthase subunit alpha, chloroplastic

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Macromolecule #9: ATP synthase subunit alpha, chloroplastic

MacromoleculeName: ATP synthase subunit alpha, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 51.798965 KDa
SequenceString: MVDFGIVFQV GDGIARIYGL EKAMSGELLE FEDGTLGIAL NLEANNVGAV LLGDGLKITE GSRVRCTGKI AEIPVGEAYL GRVVDGLAR PVDGKGAVQT KDSRAIESPA PGIVARRSVY EPLATGLVAV DAMIPVGRGQ RELIIGDRQT GKTAIAVDTI L NQKGKGVI ...String:
MVDFGIVFQV GDGIARIYGL EKAMSGELLE FEDGTLGIAL NLEANNVGAV LLGDGLKITE GSRVRCTGKI AEIPVGEAYL GRVVDGLAR PVDGKGAVQT KDSRAIESPA PGIVARRSVY EPLATGLVAV DAMIPVGRGQ RELIIGDRQT GKTAIAVDTI L NQKGKGVI CVYVAIGQKA SSVAQVLNTL KERGALDYTI IVMANANEPA TLQYLAPYTG ATLAEYFMYT GRPTLTIYDD LS KQAQAYR EMSLLLRRPP GREAYPGDVF YLHSRLLERA AKLNNALGEG SMTALPIVET QEGDVSAYIP TNVISITDGQ IFL AAGLFN SGLRPAINVG ISVSRVGSAA QPKAMKQVAG KLKLELAQFA ELEAFSQFAS DLDQATQNQL ARGARLREIL KQPQ SSPLS VEEQVASLYA GTNGYLDKLE VSQVRAYLSG LRSYLANSYP KYGEILRSTL TFTPEAEGLV KQAINEYLEE FKSQA KA

UniProtKB: ATP synthase subunit alpha, chloroplastic

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Macromolecule #10: ATP synthase subunit beta, chloroplastic

MacromoleculeName: ATP synthase subunit beta, chloroplastic / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 51.428941 KDa
SequenceString: TKNMGRIVQI IGPVLDIVFA KGQVPNIYNA LTIRAKNSAG TEMAVTCEVQ QLLGDNCVRA VSMNPTEGLM RGMEVVDTGK PLSVPVGKV TLGRIFNVLG EPVDNMGNVK VEETLPIHRT APAFVDLDTR LSIFETGIKV VDLLAPYRRG GKIGLFGGAG V GKTVLIME ...String:
TKNMGRIVQI IGPVLDIVFA KGQVPNIYNA LTIRAKNSAG TEMAVTCEVQ QLLGDNCVRA VSMNPTEGLM RGMEVVDTGK PLSVPVGKV TLGRIFNVLG EPVDNMGNVK VEETLPIHRT APAFVDLDTR LSIFETGIKV VDLLAPYRRG GKIGLFGGAG V GKTVLIME LINNIAKAHG GVSVFAGVGE RTREGNDLYT EMKESGVIVE KNLSDSKVAL VYGQMNEPPG ARMRVALTAL TM AEYFRDV NKQDVLFFID NIFRFVQAGA EVSALLGRMP SAVGYQPTLA TEMGGLQERI TSTKDGSITS IQAVYVPADD LTD PAPATT FAHLDATTVL SRNLAAKGIY PAVDPLESTS TMLQPWILGE KHYDSAQSVK KTLQRYKELQ DIIAILGLDE LSEE DRLIV ARARKIERFL SQPFFVAEVF TGSPGKYVSL AETIEGFGKI FAGELDDLPE QAFYLVGNIT EAISKAASLK

UniProtKB: ATP synthase subunit beta, chloroplastic

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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

Concentration8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64764
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)

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