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- EMDB-60876: Chloroflexus aurantiacus ATP synthase, state 3, focused refinemen... -

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Basic information

Entry
Database: EMDB / ID: EMD-60876
TitleChloroflexus aurantiacus ATP synthase, state 3, focused refinement of FO and peripheral stalk
Map data
Sample
  • Complex: ATP synthase
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit b
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: 4.6 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: To Be Published
Title: An ATP synthase from the early photosynthetic prokaryote Chloroflexus aurantiacus has two proton-translocating a-subunits
Authors: Zhang X / Wu J / Xu X
History
DepositionJul 20, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60876.png

Downloads & links

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Map

FileDownload / File: emd_60876.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.)
0.93 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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.08502345 - 0.28829727
Average (Standard dev.)-0.00039455443 (±0.009422223)
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: #2

Fileemd_60876_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60876_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

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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 c

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

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 3 / 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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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: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42617
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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