+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26824 | |||||||||
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Title | Citrus V-ATPase State 1, Highest-Resolution Class | |||||||||
Map data | Citrus V-ATPase State 1, Highest-Resolution Class | |||||||||
Sample |
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Keywords | V-ATPase / rotary ATPase / complex / MEMBRANE PROTEIN | |||||||||
Biological species | Citrus limon (lemon) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Tan YZ / Rubinstein JL | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Structure / Year: 2022 Title: Structure of V-ATPase from citrus fruit. Authors: Yong Zi Tan / Kristine A Keon / Rana Abdelaziz / Peter Imming / Waltraud Schulze / Karin Schumacher / John L Rubinstein / Abstract: We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, ...We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, allowing structure determination of the enzyme in two rotational states. The structure defines the ATP:H ratio of the enzyme, demonstrating that it can establish a maximum ΔpH of ∼3, which is insufficient to maintain the low pH observed in the vacuoles of juice sac cells in lemons and other citrus fruit. Compared with yeast and mammalian enzymes, the membrane region of the plant V-ATPase lacks subunit f and possesses an unusual configuration of transmembrane α helices. Subunit H, which inhibits ATP hydrolysis in the isolated catalytic region of V-ATPase, adopts two different conformations in the intact complex, hinting at a role in modulating activity in the intact enzyme. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26824.map.gz | 13.9 MB | EMDB map data format | |
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Header (meta data) | emd-26824-v30.xml emd-26824.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26824_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_26824.png | 66.6 KB | ||
Filedesc metadata | emd-26824.cif.gz | 3.7 KB | ||
Others | emd_26824_additional_1.map.gz emd_26824_half_map_1.map.gz emd_26824_half_map_2.map.gz | 97.4 MB 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26824 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26824 | HTTPS FTP |
-Validation report
Summary document | emd_26824_validation.pdf.gz | 876.2 KB | Display | EMDB validaton report |
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Full document | emd_26824_full_validation.pdf.gz | 875.8 KB | Display | |
Data in XML | emd_26824_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_26824_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26824 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26824 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26824.map.gz / Format: CCP4 / Size: 15 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Citrus V-ATPase State 1, Highest-Resolution Class | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.617 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Citrus V-ATPase State 1, Highest-Resolution Class
File | emd_26824_additional_1.map | ||||||||||||
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Annotation | Citrus V-ATPase State 1, Highest-Resolution Class | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Citrus V-ATPase State 1, Highest-Resolution Class
File | emd_26824_half_map_1.map | ||||||||||||
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Annotation | Citrus V-ATPase State 1, Highest-Resolution Class | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Citrus V-ATPase State 1, Highest-Resolution Class
File | emd_26824_half_map_2.map | ||||||||||||
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Annotation | Citrus V-ATPase State 1, Highest-Resolution Class | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Citrus V-ATPase
Entire | Name: Citrus V-ATPase |
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Components |
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-Supramolecule #1: Citrus V-ATPase
Supramolecule | Name: Citrus V-ATPase / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Citrus limon (lemon) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 31.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.414211 µm / Nominal defocus min: 0.677558 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |