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- EMDB-60879: Chloroflexus aurantiacus ADP-bound ATP synthase, state 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-60879
TitleChloroflexus aurantiacus ADP-bound ATP synthase, state 3
Map data
Sample
  • Complex: ATP synthase
    • Protein or peptide: x 8 types
  • Ligand: x 4 types
KeywordsATP synthesis / proton channels / proton-motive force / proton translocation / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / : / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding ...proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / proton motive force-driven 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 / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / 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 delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / 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 delta/epsilon subunit, C-terminal domain superfamily / 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 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, F1 complex, alpha subunit nucleotide-binding domain / 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 / 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 epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit a
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsZhang X / Wu J / Xu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171227, 31870740,31570738 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure of ATP synthase from an early photosynthetic bacterium .
Authors: Xin Zhang / Jingyi Wu / Zhenzhen Min / Jiamao Wang / Xin Hong / Xinkai Pei / Zihe Rao / Xiaoling Xu /
Abstract: F-type ATP synthase (FF) catalyzes proton motive force-driven ATP synthesis in mitochondria, chloroplasts, and bacteria. Different from the mitochondrial and bacterial enzymes, FF from photosynthetic ...F-type ATP synthase (FF) catalyzes proton motive force-driven ATP synthesis in mitochondria, chloroplasts, and bacteria. Different from the mitochondrial and bacterial enzymes, FF from photosynthetic organisms have evolved diverse structural and mechanistic details to adapt to the light-dependent reactions. Although complete structure of chloroplast FF has been reported, no high-resolution structure of an FF from photosynthetic bacteria has been available. Here, we report cryo-EM structures of an intact and functionally competent FF from (FF), a filamentous anoxygenic phototrophic bacterium from the earliest branch of photosynthetic organisms. The structures of FF in its ADP-free and ADP-bound forms for three rotational states reveal a previously unrecognized architecture of ATP synthases. A pair of peripheral stalks connect to the F head through a dimer of δ-subunits, and associate with two membrane-embedded a-subunits that are asymmetrically positioned outside and clamp F's c-ring. The two a-subunits constitute two proton inlets on the periplasmic side and two proton outlets on the cytoplasmic side, endowing FF with unique proton translocation pathways that allow more protons being translocated relative to single a-subunit FF. Our findings deepen understanding of the architecture and proton translocation mechanisms of FF synthases and suggest innovative strategies for modulating their activities by altering the number of a-subunit.
History
DepositionJul 20, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60879.png

Downloads & links

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Map

FileDownload / File: emd_60879.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.2767922 - 0.57630634
Average (Standard dev.)0.0005464569 (±0.017527062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60879_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_60879_half_map_2.map
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Sample components

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Entire : ATP synthase

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

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Supramolecule #1: ATP synthase

SupramoleculeName: ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 56.56334 KDa
SequenceString: MTTITEELIA RLKQGITSGV DLQPRQVNVG TVIAVGDGVA RLSGLDQVVA SEIVEFPPKA GRNESIYGIA LNLEQDSVAA IILGDDETI EEGDMVTSTG RVISVPVGQG LLGRVVNPLG QPIDGKGPIV YEKTRPIERI APGVITRKSV DTPVQTGIIA I DALIPIGR ...String:
MTTITEELIA RLKQGITSGV DLQPRQVNVG TVIAVGDGVA RLSGLDQVVA SEIVEFPPKA GRNESIYGIA LNLEQDSVAA IILGDDETI EEGDMVTSTG RVISVPVGQG LLGRVVNPLG QPIDGKGPIV YEKTRPIERI APGVITRKSV DTPVQTGIIA I DALIPIGR GQRELIIGDR QTGKTAVAID TILNQKGQGM VCIYVAIGQR RAQVAQVVGT LERFGAMEYT IVVSATASES AA LQYIAPY AGCAMGEEIM ENGVMLNGQL VKDALIVYDD LSKHAVAYRQ VSLLLRRPPG REAYPGDVFY LHSRLLERAA RLN EEYGGG SLTALPVIET QANDVSAYIP TNVISITDGQ IYLESDLFNA GQRPALNVGI SVSRVGGAAQ TRAMRAVAGK LKGE LAQFR DLAAFAQFAS DLDATTKAQI ERGQRLQELL KQPQYQPLPV EDQVAVLYAA TNNYLDDVPV PLITKWRDDF LAFLR TAHP EVRKLIYDNR LDRKFPTPEV KEALEAAIKE FKATSNYS

UniProtKB: ATP synthase subunit alpha

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Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 51.755691 KDa
SequenceString: MPAKGVIQEI IGVVIRAKFP EDEVPEIYNA IEIPLGNGDR LVCEVQQQLG NGVVKAVAMG STDGLRRGLE VIDTGRPIAV PVGPATLGR VFNVLGDPID GMGPIGPEVE RRPIHRDPPS FEEQNTQAQI FETGIKVIDL IAPFTRGGKT AIFGGAGVGK T VVIQELIA ...String:
MPAKGVIQEI IGVVIRAKFP EDEVPEIYNA IEIPLGNGDR LVCEVQQQLG NGVVKAVAMG STDGLRRGLE VIDTGRPIAV PVGPATLGR VFNVLGDPID GMGPIGPEVE RRPIHRDPPS FEEQNTQAQI FETGIKVIDL IAPFTRGGKT AIFGGAGVGK T VVIQELIA NIAKEQSGFS VFAGVGERSR EGNDLIHEMK EARIDENTTV FDKTVMVFGQ MNEPPGARLR VGLTALTMAE YF RDEGRDI LLFIDNIFRF VQAGSEVSSL LGRMPSQVGY QPTLGTEMGE LQERITSTKR GSITSMQAVY VPADDYTDPA PAT VFSHLD ATISLERSIA ERAIFPAVDP LASTSRILDP NIVGEEHYRV AQEVKRVLQR YKDLKDIIAI LGMEELSDED KLTV QRARK IELFFSQPFT VAQQFTGRPG KYVPVKKTVE SFARLLNGEG DHIPESFFYM QGDFDDVLAA YEASQK

UniProtKB: ATP synthase subunit beta

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Macromolecule #3: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 15.694111 KDa
SequenceString:
MPIHLEIVTA ERVILSDDVD MISAPTKDGR VGILPRHAPL MTILEPGELD IIKNGERTPF AVSGGFMEVL PHRVTILADT VERADEIDE ARAEQARAEA EARRREAQSE RDMALAEAKL RKEMVRLRVA QLHKIKRRQS

UniProtKB: ATP synthase epsilon chain

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Macromolecule #4: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 16.552895 KDa
SequenceString:
MATTIDARAL AAPLVEALLT TAAEQIRAAA PRIAGLSASE AAAVLPADLL PQVRNFLLTM AKEGLTGELN AVAAALPGYL ETGSRAVDA SVTSAIELSA EQKERITREL QQRYGDVHVT YHVDPTLIGG LIIRVGDQVL DNSLRARLSA IQRVLQAS

UniProtKB: ATP synthase subunit delta

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Macromolecule #5: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 32.118955 KDa
SequenceString: MPSSREIKRR IRSVKNVAQI TRAMEMVSAS KMRRAQRNVL ATRPYADRMR EVMANLTARV VGAARRGTLL EKRETVKSVA LLVVTPDRG LCGSLVANVL RRAGRFITEQ RAMGRTVDVY TFGRKGRDFF LRTGFAPAGE ATRLGDAPKL EAILGVAISA I NGFQSGKY ...String:
MPSSREIKRR IRSVKNVAQI TRAMEMVSAS KMRRAQRNVL ATRPYADRMR EVMANLTARV VGAARRGTLL EKRETVKSVA LLVVTPDRG LCGSLVANVL RRAGRFITEQ RAMGRTVDVY TFGRKGRDFF LRTGFAPAGE ATRLGDAPKL EAILGVAISA I NGFQSGKY DELYIIYSEF INTLVQRPAI KQLLPVESPD ISTTTNVDYT YEPGEEEVLN SILPRYVETQ IYQAVLESIA SE HSARMVA MRNATNNAKD LVRDLTLSFN KARQAAITKE VSEIASGAAA LTS

UniProtKB: ATP synthase gamma chain

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Macromolecule #6: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 18.710455 KDa
SequenceString:
MEALGINPTL FIAQLINFLL LIFILRALLY RPVMNLLNER TRRIEESVRD AEKVREQLAN ARRDYEAEIA RARQEAAKIV AQAQERAKQ QEAEIIAQAR REAERLKEEA RAQAEQERIR MLSEAKSQIA DLVTLTASRV LGAELQARGH DALIAESLAA L DRRN

UniProtKB: ATP synthase subunit b

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Macromolecule #7: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 34.176105 KDa
SequenceString: MSTRTRNILI IVGALIISIA SRFFLYTGPP HVEVAAEVIF DGIPGFPITN SFVVAIIIDI FVIALAVAAT RNLQMVPRGL QNVMEFILE SLYNLFRNIN AKYVATAFPL VATIFLFVLF GNWFGLLPGV GSIGVCHEKK EEHAVVDERL ALAAPAAPLS S VAAAEGEE ...String:
MSTRTRNILI IVGALIISIA SRFFLYTGPP HVEVAAEVIF DGIPGFPITN SFVVAIIIDI FVIALAVAAT RNLQMVPRGL QNVMEFILE SLYNLFRNIN AKYVATAFPL VATIFLFVLF GNWFGLLPGV GSIGVCHEKK EEHAVVDERL ALAAPAAPLS S VAAAEGEE IHDTCAAQGK KLVPLFRAPA ADLNFTFAIA VISFVFIEYW GFRALGPGYL KKFFNTNGIM SFVGIIEFIS EL VKPFALA FRLFGNIFAG EVLLVVMAFL VPLLLPLPFY GFEVFVGFIQ ALIFALLTYA FLNIAVTGHD EEHAH

UniProtKB: ATP synthase subunit a

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Macromolecule #8: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 8 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Molecular weightTheoretical: 7.688102 KDa
SequenceString:
MEGLNLVATA LAVGLGAIGP GVGIGIIVSG AVQAIGRNPE IENRVVTYMF IGIAFTEALA IFGLVIAFLI GFGVLQ

UniProtKB: ATP synthase subunit c

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #12: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6n2y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37529
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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