[English] 日本語
Yorodumi- EMDB-12638: Structure of the fungal plasma membrane proton pump Pma1 in its a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12638 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the fungal plasma membrane proton pump Pma1 in its auto-inhibited state - monomer unit | ||||||||||||||||||
Map data | monomeric map derived from focused 3D classification and refinement of symmetry expanded particles | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Function / homology | Function and homology information P-type H+-exporting transporter / proton export across plasma membrane / P-type proton-exporting transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Neurospora crassa (fungus) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Heit S / Geurts MMG / Murphy BJ / Corey R / Mills DJ / Kuehlbrandt W / Bublitz M | ||||||||||||||||||
Funding support | United Kingdom, 5 items
| ||||||||||||||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Structure of the hexameric fungal plasma membrane proton pump in its autoinhibited state. Authors: Sabine Heit / Maxwell M G Geurts / Bonnie J Murphy / Robin A Corey / Deryck J Mills / Werner Kühlbrandt / Maike Bublitz / Abstract: The fungal plasma membrane H-ATPase Pma1 is a vital enzyme, generating a proton-motive force that drives the import of essential nutrients. Autoinhibited Pma1 hexamers in the plasma membrane of ...The fungal plasma membrane H-ATPase Pma1 is a vital enzyme, generating a proton-motive force that drives the import of essential nutrients. Autoinhibited Pma1 hexamers in the plasma membrane of starving fungi are activated by glucose signaling and subsequent phosphorylation of the autoinhibitory domain. As related P-type adenosine triphosphatases (ATPases) are not known to oligomerize, the physiological relevance of Pma1 hexamers remained unknown. We have determined the structure of hexameric Pma1 from by electron cryo-microscopy at 3.3-Å resolution, elucidating the molecular basis for hexamer formation and autoinhibition and providing a basis for structure-based drug development. Coarse-grained molecular dynamics simulations in a lipid bilayer suggest lipid-mediated contacts between monomers and a substantial protein-induced membrane deformation that could act as a proton-attracting funnel. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12638.map.gz | 163.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-12638-v30.xml emd-12638.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12638_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_12638.png | 120.7 KB | ||
Masks | emd_12638_msk_1.map | 209.3 MB | Mask map | |
Others | emd_12638_half_map_1.map.gz emd_12638_half_map_2.map.gz | 164.8 MB 164.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12638 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12638 | HTTPS FTP |
-Related structure data
Related structure data | 7nxfMC 7ny1C 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_12638.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | monomeric map derived from focused 3D classification and refinement of symmetry expanded particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_12638_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_12638_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_12638_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Monomeric subunit of the hexameric fungal plasma membrane proton ...
Entire | Name: Monomeric subunit of the hexameric fungal plasma membrane proton pump in its auto-inhibited stateMonomer |
---|---|
Components |
|
-Supramolecule #1: Monomeric subunit of the hexameric fungal plasma membrane proton ...
Supramolecule | Name: Monomeric subunit of the hexameric fungal plasma membrane proton pump in its auto-inhibited state type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Neurospora crassa (fungus) / Strain: FGSC #4761 / Location in cell: plasma membrane |
-Macromolecule #1: Plasma membrane ATPase
Macromolecule | Name: Plasma membrane ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type H+-exporting transporter |
---|---|
Source (natural) | Organism: Neurospora crassa (fungus) |
Molecular weight | Theoretical: 99.984359 KDa |
Sequence | String: MADHSASGAP ALSTNIESGK FDEKAAEAAA YQPKPKVEDD EDEDIDALIE DLESHDGHDA EEEEEEATPG GGRVVPEDML QTDTRVGLT SEEVVQRRRK YGLNQMKEEK ENHFLKFLGF FVGPIQFVME GAAVLAAGLE DWVDFGVICG LLLLNAVVGF V QEFQAGSI ...String: MADHSASGAP ALSTNIESGK FDEKAAEAAA YQPKPKVEDD EDEDIDALIE DLESHDGHDA EEEEEEATPG GGRVVPEDML QTDTRVGLT SEEVVQRRRK YGLNQMKEEK ENHFLKFLGF FVGPIQFVME GAAVLAAGLE DWVDFGVICG LLLLNAVVGF V QEFQAGSI VDELKKTLAL KAVVLRDGTL KEIEAPEVVP GDILQVEEGT IIPADGRIVT DDAFLQVDQS ALTGESLAVD KH KGDQVFA SSAVKRGEAF VVITATGDNT FVGRAAALVN AASGGSGHFT EVLNGIGTIL LILVIFTLLI VWVSSFYRSN PIV QILEFT LAITIIGVPV GLPAVVTTTM AVGAAYLAKK KAIVQKLSAI ESLAGVEILC SDKTGTLTKN KLSLHDPYTV AGVD PEDLM LTACLAASRK KKGIDAIDKA FLKSLKYYPR AKSVLSKYKV LQFHPFDPVS KKVVAVVESP QGERITCVKG APLFV LKTV EEDHPIPEEV DQAYKNKVAE FATRGFRSLG VARKRGEGSW EILGIMPCMD PPRHDTYKTV CEAKTLGLSI KMLTGD AVG IARETSRQLG LGTNIYNAER LGLGGGGDMP GSEVYDFVEA ADGFAEVFPQ HKYNVVEILQ QRGYLVAMTG DGVNDAP SL KKADTGIAVE GSSDAARSAA DIVFLAPGLG AIIDALKTSR QIFHRMYAYV VYRIALSIHL EIFLGLWIAI LNRSLNIE L VVFIAIFADV ATLAIAYDNA PYSQTPVKWN LPKLWGMSVL LGVVLAVGTW ITVTTMYAQG ENGGIVQNFG NMDEVLFLQ ISLTENWLIF ITRANGPFWS SIPSWQLSGA IFLVDILATC FTIWGWFEHS DTSIVAVVRI WIFSFGIFCI MGGVYYILQD SVGFDNLMH GKSPKGNQKQ RSLEDFVVSL QRVSTQHEKS Q |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: K |
---|---|
Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 6.5 |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |