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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Citrus V-ATPase State 2, H in contact with subunits AB | |||||||||
![]() | Citrus V-ATPase State 2, H in contact with subunits AB | |||||||||
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![]() | V-ATPase / rotary ATPase / complex / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() 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 / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / plant-type vacuole / vacuole / vacuolar acidification / vacuolar membrane ...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 / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / plant-type vacuole / vacuole / vacuolar acidification / vacuolar membrane / fungal-type vacuole membrane / ATP metabolic process / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / transmembrane transport / ATPase binding / lysosomal membrane / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Tan YZ / Rubinstein JL | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 93.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31 KB 31 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 53.3 KB | ||
Filedesc metadata | ![]() | 8.2 KB | ||
Others | ![]() ![]() ![]() | 97.4 MB 95.6 MB 95.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uwdMC ![]() 7uw9C ![]() 7uwaC ![]() 7uwbC ![]() 7uwcC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Citrus V-ATPase State 2, 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: Citrus V-ATPase State 2, H in contact with subunits AB
File | emd_26829_additional_1.map | ||||||||||||
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Annotation | Citrus V-ATPase State 2, H in contact with subunits AB | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Citrus V-ATPase State 2, H in contact with subunits AB
File | emd_26829_half_map_1.map | ||||||||||||
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Annotation | Citrus V-ATPase State 2, H in contact with subunits AB | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Citrus V-ATPase State 2, H in contact with subunits AB
File | emd_26829_half_map_2.map | ||||||||||||
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Annotation | Citrus V-ATPase State 2, H in contact with subunits AB | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Citrus V-ATPase
+Supramolecule #1: Citrus V-ATPase
+Macromolecule #1: V-type proton ATPase subunit H
+Macromolecule #2: V-type proton ATPase catalytic subunit A
+Macromolecule #3: Vacuolar proton pump subunit B
+Macromolecule #4: V-type proton ATPase subunit E
+Macromolecule #5: V-type proton ATPase subunit G
+Macromolecule #6: V-type proton ATPase subunit D
+Macromolecule #7: V-type proton ATPase subunit F
+Macromolecule #8: V-type proton ATPase subunit C
+Macromolecule #9: V-type proton ATPase subunit a
+Macromolecule #10: V-type proton ATPase subunit AP1 fragment
+Macromolecule #11: Vacuolar membrane ATPase subunit c
+Macromolecule #12: V-type proton ATPase subunit
+Macromolecule #13: V-type proton ATPase subunit e1
+Macromolecule #14: V-type proton ATPase subunit c1
+Macromolecule #15: V-type proton ATPase subunit AP2 fragment
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |