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Open data
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Basic information
Entry | Database: PDB / ID: 7unf | ||||||||||||
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Title | CryoEM structure of a mEAK7 bound human V-ATPase complex | ||||||||||||
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![]() | PROTON TRANSPORT / mTOR signaling | ||||||||||||
Function / homology | ![]() proton-transporting two-sector ATPase complex / renal tubular secretion / Blockage of phagosome acidification / Ion channel transport / intracellular pH reduction / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / synaptic vesicle lumen acidification ...proton-transporting two-sector ATPase complex / renal tubular secretion / Blockage of phagosome acidification / Ion channel transport / intracellular pH reduction / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / Golgi lumen acidification / proton-transporting V-type ATPase, V0 domain / Transferrin endocytosis and recycling / extrinsic component of synaptic vesicle membrane / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / XBP1(S) activates chaperone genes / Amino acids regulate mTORC1 / regulation of pH / proton-transporting V-type ATPase complex / ROS and RNS production in phagocytes / protein localization to cilium / Nef Mediated CD4 Down-regulation / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / azurophil granule membrane / proton transmembrane transporter activity / autophagosome membrane / microvillus / tertiary granule membrane / ATPase activator activity / ficolin-1-rich granule membrane / positive regulation of Wnt signaling pathway / RHOA GTPase cycle / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / specific granule membrane / enzyme regulator activity / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / Insulin receptor recycling / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / ossification / receptor-mediated endocytosis / secretory granule / brush border membrane / sensory perception of sound / transmembrane transport / synaptic vesicle membrane / small GTPase binding / cilium / endocytosis / phagocytic vesicle membrane / melanosome / apical part of cell / signaling receptor activity / ATPase binding / intracellular iron ion homeostasis / membrane => GO:0016020 / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å | ||||||||||||
![]() | Wang, R. / Li, X. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of mEAK7-mediated human V-ATPase regulation. Authors: Rong Wang / Yu Qin / Xiao-Song Xie / Xiaochun Li / ![]() Abstract: The activity of V-ATPase is well-known to be regulated by reversible dissociation of its V and V domains in response to growth factor stimulation, nutrient sensing, and cellular differentiation. The ...The activity of V-ATPase is well-known to be regulated by reversible dissociation of its V and V domains in response to growth factor stimulation, nutrient sensing, and cellular differentiation. The molecular basis of its regulation by an endogenous modulator without affecting V-ATPase assembly remains unclear. Here, we discover that a lysosome-anchored protein termed (mammalian Enhancer-of-Akt-1-7 (mEAK7)) binds to intact V-ATPase. We determine cryo-EM structure of human mEAK7 in complex with human V-ATPase in native lipid-containing nanodiscs. The structure reveals that the TLDc domain of mEAK7 engages with subunits A, B, and E, while its C-terminal domain binds to subunit D, presumably blocking V-V torque transmission. Our functional studies suggest that mEAK7, which may act as a V-ATPase inhibitor, does not affect the activity of V-ATPase in vitro. However, overexpression of mEAK7 in HCT116 cells that stably express subunit a4 of V-ATPase represses the phosphorylation of ribosomal protein S6. Thus, this finding suggests that mEAK7 potentially links mTOR signaling with V-ATPase 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 | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 202.5 KB | Display | |
Data in CIF | ![]() | 321.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26623MC ![]() 7uneC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-V-type proton ATPase ... , 14 types, 30 molecules aLMNOPQDbcdefgFCHkms8923456701
#1: Protein | Mass: 98530.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||||||||||||||||||||
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#3: Protein | Mass: 68379.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P38606, H+-transporting two-sector ATPase #4: Protein | Mass: 56561.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 28311.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 26183.346 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 13781.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | | Mass: 13388.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | | Mass: 43999.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | | Mass: 55949.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | | Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | | Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | | Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 3 types, 3 molecules Unr
#2: Protein | Mass: 51096.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#13: Protein | Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q6P5S7, Hydrolases; Acting on ester bonds |
#15: Protein | Mass: 38421.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 3 types, 8 molecules ![](data/chem/img/NAG.gif)
#18: Polysaccharide | alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#19: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
#21: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 10 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/POV.gif)
![](data/chem/img/POV.gif)
#20: Chemical | ChemComp-ADP / |
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#22: Chemical | ChemComp-POV / ( |
-Details
Has ligand of interest | N |
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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: CryoEM structure of mEAK7 bound human V-ATPase complex Type: COMPLEX / Entity ID: #1-#17 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
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: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24984 / Symmetry type: POINT |