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- EMDB-60885: Chloroflexus aurantiacus ADP-bound ATP synthase, state 3, focused... -

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Basic information

Entry
Database: EMDB / ID: EMD-60885
TitleChloroflexus aurantiacus ADP-bound ATP synthase, state 3, focused refinement of FO and peripheral stalk
Map data
Sample
  • Complex: ATP synthase
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit c
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 motive force-driven ATP synthesis / : / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
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, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily ...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, F0 complex, subunit C, bacterial/chloroplast / 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. / 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. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
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: 5.18 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_60885.png

Downloads & links

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Map

FileDownload / File: emd_60885.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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Others
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

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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-0.097102135 - 0.21702932
Average (Standard dev.)-0.0000775363 (±0.0077513047)
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_60885_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_60885_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 b
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit c

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Supramolecule #1: ATP synthase

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

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Macromolecule #1: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 1 / 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 #2: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 2 / 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 #3: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 3 / 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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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: 5.18 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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