+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26826 | |||||||||
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Title | Citrus V-ATPase State 1, H in contact with subunits AB | |||||||||
Map data | Citrus V-ATPase State 1, H in contact with subunits AB | |||||||||
Sample |
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Function / homology | Function and homology information proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase, V0 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / vacuole / vacuolar membrane / ATP metabolic process ...proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase, V0 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / vacuole / vacuolar membrane / ATP metabolic process / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Citrus limon (lemon) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Abdelaziz RA / Keon KA / Schulze WX / Schumacher K / 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_26826.map.gz | 94 MB | EMDB map data format | |
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Header (meta data) | emd-26826-v30.xml emd-26826.xml | 30.3 KB 30.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26826_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_26826.png | 61.8 KB | ||
Others | emd_26826_additional_1.map.gz emd_26826_half_map_1.map.gz emd_26826_half_map_2.map.gz | 97.4 MB 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26826 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26826 | HTTPS FTP |
-Related structure data
Related structure data | 7uwaMC 7uw9C 7uwbC 7uwcC 7uwdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26826.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Citrus V-ATPase State 1, H in contact with subunits AB | ||||||||||||||||||||
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: Globally refined map
File | emd_26826_additional_1.map | ||||||||||||
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Annotation | Globally refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Citrus V-ATPase State 1, H in contact with subunits AB
File | emd_26826_half_map_1.map | ||||||||||||
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Annotation | Citrus V-ATPase State 1, H in contact with subunits AB | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Citrus V-ATPase State 1, H in contact with subunits AB
File | emd_26826_half_map_2.map | ||||||||||||
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Annotation | Citrus V-ATPase State 1, H in contact with subunits AB | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Citrus V-ATPase
+Supramolecule #1: Citrus V-ATPase
+Macromolecule #1: V-type proton ATPase catalytic subunit A
+Macromolecule #2: V-type proton ATPase subunit B2
+Macromolecule #3: V-type proton ATPase subunit D
+Macromolecule #4: V-type proton ATPase subunit F
+Macromolecule #5: V-type proton ATPase subunit AP1 fragment
+Macromolecule #6: V-type proton ATPase subunit c"
+Macromolecule #7: V-type proton ATPase subunit d2
+Macromolecule #8: V-type proton ATPase subunit c
+Macromolecule #9: V-type proton ATPase subunit AP2 fragment
+Macromolecule #10: V-type proton ATPase subunit E
+Macromolecule #11: V-type proton ATPase subunit G
+Macromolecule #12: V-type proton ATPase subunit C
+Macromolecule #13: V-type proton ATPase subunit a3
+Macromolecule #14: V-type proton ATPase subunit e1
+Macromolecule #15: V-type proton ATPase subunit H
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.414211 µm / Nominal defocus min: 0.677558 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 31.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |