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Open data
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Basic information
Entry | Database: PDB / ID: 7u8p | |||||||||||||||
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Title | Structure of porcine kidney V-ATPase with SidK, Rotary State 1 | |||||||||||||||
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![]() | MEMBRANE PROTEIN / proton translocation / complex | |||||||||||||||
Function / homology | ![]() ROS and RNS production in phagocytes / RHOA GTPase cycle / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Insulin receptor recycling / transporter activator activity / 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 / Insulin receptor recycling / transporter activator activity / 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 / proton-transporting two-sector ATPase complex, catalytic domain / plasma membrane proton-transporting V-type ATPase complex / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / proton-transporting V-type ATPase complex / cell projection organization / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / vacuolar membrane / osteoclast development / autophagosome membrane / microvillus / ATPase activator activity / positive regulation of Wnt signaling pathway / transmembrane transporter complex / ATP metabolic process / H+-transporting two-sector ATPase / transport vesicle / proton transmembrane transport / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / synaptic vesicle membrane / small GTPase binding / melanosome / presynapse / signaling receptor activity / ATPase binding / intracellular iron ion homeostasis / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | Tan, Y.Z. / Keon, K.A. | |||||||||||||||
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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 200.2 KB | Display | |
Data in CIF | ![]() | 327.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26386MC ![]() 7u8oC ![]() 7u8qC ![]() 7u8rC M: map data used to model this data 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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Assembly
Deposited unit | ![]()
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1 |
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Components
-V-type proton ATPase ... , 12 types, 26 molecules ABCGHIJKLMNOTabdeghijklmno
#1: Protein | Mass: 68393.844 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q29048, H+-transporting two-sector ATPase #3: Protein | | Mass: 44066.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 28301.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 26162.373 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 13403.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 13748.474 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | | Mass: 55917.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | | Mass: 96365.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | | Mass: 21530.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | | Mass: 9343.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 15639.677 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 5 types, 9 molecules DEFQRScfp
#2: Protein | Mass: 57162.859 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 38539.371 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #12: Protein | | Mass: 51547.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | | Mass: 11016.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | | Mass: 39200.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ADP.gif)
#18: Chemical | ChemComp-ADP / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Porcine kidney V-ATPase with SidK, Rotary State 1 / Type: COMPLEX / Entity ID: #1-#17 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3911.445 nm / Nominal defocus min: 100 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24327 / Symmetry type: POINT |