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- EMDB-12425: Mycobacterium smegmatis ATP synthase Fo combined class 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-12425
TitleMycobacterium smegmatis ATP synthase Fo combined class 3
Map dataMsmeg ATP synthase Fo combined class 3 map
Sample
  • Complex: Mycobacterium smegmatis ATP synthase
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit b-delta
    • Protein or peptide: ATP synthase subunit b
Keywordscomplex / synthase / HYDROLASE
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / 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. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / 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-delta / ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit a
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsMontgomery MG / Petri J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00015/8 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structure of the ATP synthase from provides targets for treating tuberculosis.
Authors: Martin G Montgomery / Jessica Petri / Tobias E Spikes / John E Walker /
Abstract: The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from This analysis confirms features in a prior description of the structure of the enzyme, ...The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a "fail-safe" mechanism involving the b'-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated "fail-safe" mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel.
History
DepositionFeb 17, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7njw
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12425.png

Downloads & links

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Map

FileDownload / File: emd_12425.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMsmeg ATP synthase Fo combined class 3 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. Å		0.83 Å/pix.
x 500 pix.
= 415. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.02298395 - 0.05030181
Average (Standard dev.)0.000048859005 (±0.0007791598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 415.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z415.000415.000415.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0230.0500.000

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Supplemental data

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Sample components

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Entire : Mycobacterium smegmatis ATP synthase

EntireName: Mycobacterium smegmatis ATP synthase
Components
  • Complex: Mycobacterium smegmatis ATP synthase
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit b-delta
    • Protein or peptide: ATP synthase subunit b

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Supramolecule #1: Mycobacterium smegmatis ATP synthase

SupramoleculeName: Mycobacterium smegmatis ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 547 KDa

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Macromolecule #1: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 8.597982 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MDLDPNAIIT AGALIGGGLI MGGGAIGAGI GDGIAGNALI SGIARQPEAQ GRLFTPFFIT VGLVEAAYFI NLAFMALFVF ATPGLQ

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: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 27.568482 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MLAAEEGGAA IHVGHHTLVF ELFGMTFNGD TILATAVTAV IVIALAFYLR AKVTSTGVPS GVQLFWEALT IQMRQQIEGS IGMKIAPFV LPLSVTIFVF ILISNWLAVL PLQYGGADGA AAELYKAPAS DINFVLALAL FVFVCYHAAG IWRRGIVGHP I KVVKGHVA ...String:
MLAAEEGGAA IHVGHHTLVF ELFGMTFNGD TILATAVTAV IVIALAFYLR AKVTSTGVPS GVQLFWEALT IQMRQQIEGS IGMKIAPFV LPLSVTIFVF ILISNWLAVL PLQYGGADGA AAELYKAPAS DINFVLALAL FVFVCYHAAG IWRRGIVGHP I KVVKGHVA FLAPINIVEE LAKPISLALR LFGNIFAGGI LVALIAMFPW YIQWFPNAVW KTFDLFVGLI QAFIFSLLTI LY FSQSMEL DHEDH

UniProtKB: ATP synthase subunit a

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Macromolecule #3: ATP synthase subunit b-delta

MacromoleculeName: ATP synthase subunit b-delta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 47.504723 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MSIFIGQLIG FAVIAFIIVK WVVPPVRTLM RNQQEAVRAA LAESAEAAKK LADADAMHAK ALADAKAESE KVTEEAKQDS ERIAAQLSE QAGSEAERIK AQGAQQIQLM RQQLIRQLRT GLGAEAVNKA AEIVRAHVAD PQAQSATVDR FLSELEQMAP S SVVIDTAA ...String:
MSIFIGQLIG FAVIAFIIVK WVVPPVRTLM RNQQEAVRAA LAESAEAAKK LADADAMHAK ALADAKAESE KVTEEAKQDS ERIAAQLSE QAGSEAERIK AQGAQQIQLM RQQLIRQLRT GLGAEAVNKA AEIVRAHVAD PQAQSATVDR FLSELEQMAP S SVVIDTAA TSRLRAASRQ SLAALVEKFD SVAGGLDADG LTNLADELAS VAKLLLSETA LNKHLAEPTD DSAPKVRLLE RL LSDKVSA TTLDLLRTAV SNRWSTESNL IDAVEHTARL ALLKRAEIAG EVDEVEEQLF RFGRVLDAEP RLSALLSDYT TPA EGRVAL LDKALTGRPG VNQTAAALLS QTVGLLRGER ADEAVIDLAE LAVSRRGEVV AHVSAAAELS DAQRTRLTEV LSRI YGRPV SVQLHVDPEL LGGLSITVGD EVIDGSIASR LAAAQTGLPD

UniProtKB: ATP synthase subunit b-delta

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Macromolecule #4: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 19.01817 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MGEFSATILA ASQAAEEGGG GSNFLIPNGT FFAVLIIFLI VLGVISKWVV PPISKVLAER EAMLAKTAAD NRKSAEQVAA AQADYEKEM AEARAQASAL RDEARAAGRS VVDEKRAQAS GEVAQTLTQA DQQLSAQGDQ VRSGLESSVD GLSAKLASRI L GVDVNSGG TQHHHHHHHH HH

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: GATAN K3 (6k x 4k) / Average electron dose: 59.86 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25724
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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