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Open data
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Basic information
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Title | Structure of porcine kidney V-ATPase with SidK, Rotary State 3 | |||||||||||||||
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![]() | proton translocation / ![]() ![]() | |||||||||||||||
Function / homology | ![]() ROS and RNS production in phagocytes / RHOA GTPase cycle / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / transporter activator activity / Insulin receptor recycling / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification ...ROS and RNS production in phagocytes / RHOA GTPase cycle / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / transporter activator activity / Insulin receptor recycling / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / proton-transporting V-type ATPase, V0 domain / plasma membrane proton-transporting V-type ATPase complex / proton-transporting two-sector ATPase complex, catalytic domain / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / cell projection organization / vacuolar acidification / dendritic spine membrane / regulation of cellular pH / vacuolar membrane / osteoclast development / transmembrane transporter complex / ATPase activator activity / autophagosome membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
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Method | ![]() ![]() | |||||||||||||||
![]() | Tan YZ | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7. Authors: Yong Zi Tan / Yazan M Abbas / Jing Ze Wu / Di Wu / Kristine A Keon / Geoffrey G Hesketh / Stephanie A Bueler / Anne-Claude Gingras / Carol V Robinson / Sergio Grinstein / John L Rubinstein / ![]() ![]() Abstract: V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins ...V-ATPases are rotary proton pumps that serve as signaling hubs with numerous protein binding partners. CryoEM with exhaustive focused classification allowed detection of endogenous proteins associated with porcine kidney V-ATPase. An extra C subunit was found in ∼3% of complexes, whereas ∼1.6% of complexes bound mEAK-7, a protein with proposed roles in dauer formation in nematodes and mTOR signaling in mammals. High-resolution cryoEM of porcine kidney V-ATPase with recombinant mEAK-7 showed that mEAK-7's TLDc domain interacts with V-ATPase's stator, whereas its C-terminal α helix binds V-ATPase's rotor. This crosslink would be expected to inhibit rotary catalysis. However, unlike the yeast TLDc protein Oxr1p, exogenous mEAK-7 does not inhibit V-ATPase and mEAK-7 overexpression in cells does not alter lysosomal or phagosomal pH. Instead, cryoEM suggests that the mEAK-7:V-ATPase interaction is disrupted by ATP-induced rotation of the rotor. Comparison of Oxr1p and mEAK-7 binding explains this difference. These results show that V-ATPase binding by TLDc domain proteins can lead to effects ranging from strong inhibition to formation of labile interactions that are sensitive to the enzyme's activity. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 35.6 KB 35.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.4 KB | Display | ![]() |
Images | ![]() | 49.4 KB | ||
Filedesc metadata | ![]() | 9.9 KB | ||
Others | ![]() ![]() ![]() | 97.4 MB 95.6 MB 95.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u8rMC ![]() 7u8oC ![]() 7u8pC ![]() 7u8qC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data size: 12.7 TB Data #1: Unaligned multiframe movies of Pig Kidney V-ATPase bound to mEAK-7 collected using Tundra [micrographs - multiframe] Data #2: Aligned and dose-weighted micrographs of Pig Kidney V-ATPase bound to mEAK-7 collected using Tundra [micrographs - single frame] Data #3: Polished particles of Pig Kidney V-ATPase bound to mEAK-7 collected using Tundra [picked particles - single frame - processed] Data #4: Unaligned multiframe movies of Pig Kidney V-ATPase bound to mEAK-7 collected using Titan Krios and Falcon4 [micrographs - multiframe] Data #5: Aligned and dose-weighted micrographs of Pig Kidney V-ATPase bound to mEAK-7 collected using Titan Krios and Falcon4 [micrographs - single frame] Data #6: Polished particles of Pig Kidney V-ATPase bound to mEAK-7 collected using Titan Krios and Falcon4 [picked particles - multiframe - processed] Data #7: Unaligned multiframe movies of Pig Kidney V-ATPase bound to mEAK-7deltaCterm collected using Titan Krios and Falcon4 [micrographs - multiframe] Data #8: Aligned and dose-weighted micrographs of Pig Kidney V-ATPase bound to mEAK-7deltaCterm collected using Titan Krios and Falcon4 [micrographs - single frame] Data #9: Polished particles of Pig Kidney V-ATPase bound to mEAK-7deltaCterm collected using Titan Krios and Falcon4 [picked particles - single frame - processed] Data #10: Unaligned multiframe movies of Pig Kidney V-ATPase bound to mEAK-7 with ATP collected using Titan Krios and Falcon4 [micrographs - multiframe] Data #11: Aligned and dose-weighted micrographs of Pig Kidney V-ATPase bound to mEAK-7 with ATP collected using Titan Krios and Falcon4 [micrographs - single frame] Data #12: Polished particles of Pig Kidney V-ATPase bound to mEAK-7 with ATP collected using Titan Krios and Falcon4 [picked particles - single frame - processed] Data #13: Unaligned multiframe movies of Pig Kidney V-ATPase bound to mEAK-7 with EDTA/EGTA collected using Titan Krios and Falcon4 [micrographs - multiframe] Data #14: Aligned and dose-weighted micrographs of Pig Kidney V-ATPase bound to mEAK-7 with EDTA/EGTA collected using Titan Krios and Falcon4 [micrographs - single frame] Data #15: Polished particles of Pig Kidney V-ATPase bound to mEAK-7 with EDTA/EGTA collected using Titan Krios and Falcon4 [picked particles - single frame - processed] Data #16: Unaligned multiframe movies of Pig Kidney V-ATPase bound to mEAK-7 with Calcium collected using Glacios with Selectris X and Falcon 4 [micrographs - multiframe] Data #17: Aligned and dose-weighted micrographs of Pig Kidney V-ATPase bound to mEAK-7 with Calcium collected using Glacios with Selectris X and Falcon 4 [micrographs - single frame] Data #18: Polished particles of Pig Kidney V-ATPase bound to mEAK-7 with Calcium collected using Glacios with Selectris X and Falcon 4 [picked particles - single frame - processed]) |
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Links
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Related items in Molecule of the Month |
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Map
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Annotation | Map used for model building. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.52801 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: V-ATPase with SidK, Rotary State 3
File | emd_26388_additional_1.map | ||||||||||||
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Annotation | V-ATPase with SidK, Rotary State 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: V-ATPase with SidK, Rotary State 3
File | emd_26388_half_map_1.map | ||||||||||||
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Annotation | V-ATPase with SidK, Rotary State 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: V-ATPase with SidK, Rotary State 3
File | emd_26388_half_map_2.map | ||||||||||||
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Annotation | V-ATPase with SidK, Rotary State 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Porcine kidney V-ATPase with SidK, Rotary State 3
+Supramolecule #1: Porcine kidney V-ATPase with SidK, Rotary State 3
+Macromolecule #1: V-type proton ATPase catalytic subunit A
+Macromolecule #2: Vacuolar proton pump subunit B
+Macromolecule #3: V-type proton ATPase subunit C
+Macromolecule #4: V-type proton ATPase subunit D
+Macromolecule #5: V-type proton ATPase subunit E 1
+Macromolecule #6: V-type proton ATPase subunit F
+Macromolecule #7: V-type proton ATPase subunit G
+Macromolecule #8: Bacterial effector protein SidK
+Macromolecule #9: V-type proton ATPase subunit H
+Macromolecule #10: V-type proton ATPase subunit a
+Macromolecule #11: V-type proton ATPase 21 kDa proteolipid subunit isoform 1
+Macromolecule #12: ATPase H+ transporting accessory protein 1
+Macromolecule #13: V-type proton ATPase subunit
+Macromolecule #14: V-type proton ATPase subunit
+Macromolecule #15: Ribonuclease kappa
+Macromolecule #16: V-type proton ATPase proteolipid subunit
+Macromolecule #17: ATPase H(+)-transporting lysosomal accessory protein 2
+Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | ![]() |
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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 | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |