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- EMDB-22312: Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP... -

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Basic information

Entry
Database: EMDB / ID: EMD-22312
TitleCryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 2
Map dataLocally sharpened map
Sample
  • Complex: ATP synthase from Mycobacterium smegmatis
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit b
  • Protein or peptide: ATP synthase subunit b-delta
  • Protein or peptide: ATP synthase subunit c
KeywordsBedaquiline / Sirturo / TMC207 / T207910 / ATP synthase / mycobacteria / tuberculosis / TRANSLOCASE
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / membrane => GO:0016020 / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / ATP hydrolysis activity ...proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / membrane => GO:0016020 / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP 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, 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, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / 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 b / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit b-delta ...ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit b / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit b-delta / ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit a / ATP synthase subunit c
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGuo H / Courbon GM
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canadian Institutes of Health Research (CIHR)PJT156261 Canada
Citation
Journal: Nature / Year: 2021
Title: Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline.
Authors: Hui Guo / Gautier M Courbon / Stephanie A Bueler / Juntao Mai / Jun Liu / John L Rubinstein /
Abstract: Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics. The bacterium Mycobacterium tuberculosis (which causes tuberculosis) ...Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics. The bacterium Mycobacterium tuberculosis (which causes tuberculosis) can survive low-energy conditions, allowing infections to remain dormant and decreasing their susceptibility to many antibiotics. Bedaquiline was developed in 2005 from a lead compound identified in a phenotypic screen against Mycobacterium smegmatis. This drug can sterilize even latent M. tuberculosis infections and has become a cornerstone of treatment for multidrug-resistant and extensively drug-resistant tuberculosis. Bedaquiline targets the mycobacterial ATP synthase, which is an essential enzyme in the obligate aerobic Mycobacterium genus, but how it binds the intact enzyme is unknown. Here we determined cryo-electron microscopy structures of M. smegmatis ATP synthase alone and in complex with bedaquiline. The drug-free structure suggests that hook-like extensions from the α-subunits prevent the enzyme from running in reverse, inhibiting ATP hydrolysis and preserving energy in hypoxic conditions. Bedaquiline binding induces large conformational changes in the ATP synthase, creating tight binding pockets at the interface of subunits a and c that explain the potency of this drug as an antibiotic for tuberculosis.
#1: Journal: Biorxiv / Year: 2020
Title: Structure of mycobacterial ATP synthase with the TB drug bedaquiline
Authors: Guo H / Courbon GM / Bueler SA / Mai J / Liu J / Rubinstein JL
History
DepositionJul 18, 2020-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jg6
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22312.png

Downloads & links

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Map

FileDownload / File: emd_22312.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened map
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-0.15881895 - 19.579205000000002
Average (Standard dev.)0.01389256 (±0.32988906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.15919.5790.014

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Supplemental data

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Mask #1

Fileemd_22312_msk_1.map
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Additional map: Unsharpened map

Fileemd_22312_additional.map
AnnotationUnsharpened map
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Additional map: Unsharpened map

Fileemd_22312_additional_1.map
AnnotationUnsharpened map
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Half map: Half map 1

Fileemd_22312_half_map_1.map
AnnotationHalf map 1
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Half map: Half map 2

Fileemd_22312_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : ATP synthase from Mycobacterium smegmatis

EntireName: ATP synthase from Mycobacterium smegmatis
Components
  • Complex: ATP synthase from Mycobacterium smegmatis
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit b
  • Protein or peptide: ATP synthase subunit b-delta
  • Protein or peptide: ATP synthase subunit c

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Supramolecule #1: ATP synthase from Mycobacterium smegmatis

SupramoleculeName: ATP synthase from Mycobacterium smegmatis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 58.951461 KDa
SequenceString: MAELTISAAD IEGAIEDYVS SFSADTEREE IGTVIDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD EHSVGAVILG EFEKIEEGQ QVKRTGEVLS VPVGDAFLGR VVNPLGQPID GQGDIAAETR RALELQAPSV VQRQSVSEPL QTGIKAIDAM T PIGRGQRQ ...String:
MAELTISAAD IEGAIEDYVS SFSADTEREE IGTVIDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD EHSVGAVILG EFEKIEEGQ QVKRTGEVLS VPVGDAFLGR VVNPLGQPID GQGDIAAETR RALELQAPSV VQRQSVSEPL QTGIKAIDAM T PIGRGQRQ LIIGDRKTGK TAVCVDTILN QREAWLTGDP KQQVRCVYVA IGQKGTTIAS VKRALEEGGA MEYTTIVAAP AS DAAGFKW LAPYTGSAIG QHWMYNGKHV LIVFDDLSKQ ADAYRAISLL LRRPPGREAF PGDVFYLHSR LLERCAKLSD ELG GGSMTG LPIIETKAND ISAFIPTNVI SITDGQCFLE SDLFNQGVRP AINVGVSVSR VGGAAQIKAM KEVAGSLRLD LSQY RELEA FAAFASDLDA ASKAQLDRGA RLVELLKQPQ YSPLAVEEQV VAIFLGTQGH LDSVPVEDVQ RFESELLEHV KASHS DIFD GIRETKKLSE EAEEKLVSVI NEFKKGFQAS DGSSVVVSEN AEALDPEDLE KESVKVRKPA PKKA

UniProtKB: ATP synthase subunit alpha

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Macromolecule #2: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 58.509234 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)SADTERE EIGTVIDAGD GIAHVEGLPS VMTQELLEFP GGVLGVALNL DEH SVGAVI LGEFEKIEEG ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)SADTERE EIGTVIDAGD GIAHVEGLPS VMTQELLEFP GGVLGVALNL DEH SVGAVI LGEFEKIEEG QQVKRTGEVL SVPVGDAFLG RVVNPLGQPI DGQGDIAAET RRALELQAPS VVQRQSVSEP LQTG IKAID AMTPIGRGQR QLIIGDRKTG KTAVCVDTIL NQREAWLTGD PKQQVRCVYV AIGQKGTTIA SVKRALEEGG AMEYT TIVA APASDAAGFK WLAPYTGSAI GQHWMYNGKH VLIVFDDLSK QADAYRAISL LLRRPPGREA FPGDVFYLHS RLLERC AKL SDELGGGSMT GLPIIETKAN DISAFIPTNV ISITDGQCFL ESDLFNQGVR PAINVGVSVS RVGGAAQIKA MKEVAGS LR LDLSQYRELE AFAAFASDLD AASKAQLDRG ARLVELLKQP QYSPLAVEEQ VVAIFLGTQG HLDSVPVEDV QRFESELL E HVKASHSDIF DGIRETKKLS EEAEEKLVSV INEFKKGFQA SDGSSVVVSE NAEALDPEDL EKESVKVRKP APKKA

UniProtKB: ATP synthase subunit alpha

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Macromolecule #3: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 51.670453 KDa
SequenceString: MTATAEKTAG RVVRITGPVV DVEFPRGSVP ELFNALHAEI TFGALAKTLT LEVAQHLGDS LVRCISMQPT DGLVRGVEVT DTGASISVP VGDGVKGHVF NALGDCLDDP GYGKDFEHWS IHRKPPAFSD LEPRTEMLET GLKVVDLLTP YVRGGKIALF G GAGVGKTV ...String:
MTATAEKTAG RVVRITGPVV DVEFPRGSVP ELFNALHAEI TFGALAKTLT LEVAQHLGDS LVRCISMQPT DGLVRGVEVT DTGASISVP VGDGVKGHVF NALGDCLDDP GYGKDFEHWS IHRKPPAFSD LEPRTEMLET GLKVVDLLTP YVRGGKIALF G GAGVGKTV LIQEMINRIA RNFGGTSVFA GVGERTREGN DLWVELADAN VLKDTALVFG QMDEPPGTRM RVALSALTMA EF FRDEQGQ DVLLFIDNIF RFTQAGSEVS TLLGRMPSAV GYQPTLADEM GELQERITST RGRSITSMQA VYVPADDYTD PAP ATTFAH LDATTELSRA VFSKGIFPAV DPLASSSTIL DPAIVGDEHY RVAQEVIRIL QRYKDLQDII AILGIDELSE EDKQ LVNRA RRIERFLSQN MMAAEQFTGQ PGSTVPLKET IEAFDKLTKG EFDHLPEQAF FLIGGLDDLA KKAESLGAKL

UniProtKB: ATP synthase subunit beta

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Macromolecule #4: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 33.439836 KDa
SequenceString: MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIAKAQARV EAARPYAAEI TNMLTELAGA SALDHPLLVE RKQPKRAGVL VVSSDRGLC GAYNANVLRR AEELFSLLRD EGKDPVLYVV GRKALGYFSF RQRTVVESWT GFSERPTYEN AREIADTLVN A FMAGADDE ...String:
MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIAKAQARV EAARPYAAEI TNMLTELAGA SALDHPLLVE RKQPKRAGVL VVSSDRGLC GAYNANVLRR AEELFSLLRD EGKDPVLYVV GRKALGYFSF RQRTVVESWT GFSERPTYEN AREIADTLVN A FMAGADDE GDDAGADGIL GVDELHIVFT EFRSMLSQTA VARRAAPMEV EYVGEVETGP RTLYSFEPDP ETLFDALLPR YI ATRVYAA LLEAAASESA SRRRAMKSAT DNADDLIKAL TLAANRERQA QITQEISEIV GGANALAGSK

UniProtKB: ATP synthase gamma chain

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Macromolecule #5: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 13.277741 KDa
SequenceString:
MADLNVEIVA VERELWSGPA TFVFTRTTAG EIGILPRHIP LVAQLVDDAM VRVEREGEDD LRIAVDGGFL SVTEETVRIL VENAQFESE IDADAAKEDA ASDDERTAAW GRARLRALGQ ID

UniProtKB: ATP synthase epsilon chain

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Macromolecule #6: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 27.568482 KDa
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 #7: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 17.636701 KDa
SequenceString:
MGEFSATILA ASQAAEEGGG GSNFLIPNGT FFAVLIIFLI VLGVISKWVV PPISKVLAER EAMLAKTAAD NRKSAEQVAA AQADYEKEM AEARAQASAL RDEARAAGRS VVDEKRAQAS GEVAQTLTQA DQQLSAQGDQ VRSGLESSVD GLSAKLASRI L GVDVNSGG TQ

UniProtKB: ATP synthase subunit b

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Macromolecule #8: ATP synthase subunit b-delta

MacromoleculeName: ATP synthase subunit b-delta / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 47.504723 KDa
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 #9: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 9 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 8.597982 KDa
SequenceString:
MDLDPNAIIT AGALIGGGLI MGGGAIGAGI GDGIAGNALI SGIARQPEAQ GRLFTPFFIT VGLVEAAYFI NLAFMALFVF ATPGLQ

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

Concentration6 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER/RHODIUM / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 7691 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1435679
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.11) / Number images used: 46960
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.11)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.11)
Final 3D classificationNumber classes: 3 / Avg.num./class: 236017 / Software - Name: cryoSPARC (ver. 2.11)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-7jg6:
Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 2 (backbone model)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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