+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12438 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mycobacterium smegmatis ATP synthase b-delta state 1 | |||||||||
Map data | M smegmatis ATP synthase bd-fusion combiset map | |||||||||
Sample |
| |||||||||
Keywords | complex / synthase / HYDROLASE | |||||||||
Function / homology | Function and homology information photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
Authors | Montgomery MG / Petri J | |||||||||
Funding support | United Kingdom, 2 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12438.map.gz | 10.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-12438-v30.xml emd-12438.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12438_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_12438.png | 67.4 KB | ||
Filedesc metadata | emd-12438.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12438 | HTTPS FTP |
-Validation report
Summary document | emd_12438_validation.pdf.gz | 336.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_12438_full_validation.pdf.gz | 335.6 KB | Display | |
Data in XML | emd_12438_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_12438_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12438 | HTTPS FTP |
-Related structure data
Related structure data | 7nkdMC 7njkC 7njlC 7njmC 7njnC 7njoC 7njpC 7njqC 7njrC 7njsC 7njtC 7njuC 7njvC 7njwC 7njxC 7njyC 7nk7C 7nk9C 7nkbC 7nkhC 7nkjC 7nkkC 7nklC 7nknC 7nkpC 7nkqC 7nl9C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_12438.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | M smegmatis ATP synthase bd-fusion combiset map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Mycobacterium smegmatis ATP synthase
Entire | Name: Mycobacterium smegmatis ATP synthase |
---|---|
Components |
|
-Supramolecule #1: Mycobacterium smegmatis ATP synthase
Supramolecule | Name: Mycobacterium smegmatis ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Molecular weight | Theoretical: 547 KDa |
-Macromolecule #1: ATP synthase subunit alpha
Macromolecule | Name: 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: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 58.951461 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: ATP synthase subunit beta
Macromolecule | Name: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 Details: Poor alignment on Chain F there is no sequence conflict. DSLV is from res59, RGV is from res75 Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase |
---|---|
Source (natural) | Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 51.670453 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis (bacteria) |
Sequence | String: 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 |
-Macromolecule #3: ATP synthase subunit b-delta
Macromolecule | Name: 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 weight | Theoretical: 47.504723 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis (bacteria) |
Sequence | String: 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 |
-Macromolecule #4: ATP synthase subunit b
Macromolecule | Name: ATP synthase subunit b / type: protein_or_peptide / ID: 4 / Details: C-ter 10His tag / 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 weight | Theoretical: 19.01817 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.86 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |