+Open data
-Basic information
Entry | Database: PDB / ID: 7unf | ||||||||||||
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Title | CryoEM structure of a mEAK7 bound human V-ATPase complex | ||||||||||||
Components |
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Keywords | PROTON TRANSPORT / mTOR signaling | ||||||||||||
Function / homology | Function and homology information proton-transporting two-sector ATPase complex / renal tubular secretion / Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / plasma membrane proton-transporting V-type ATPase complex ...proton-transporting two-sector ATPase complex / renal tubular secretion / Blockage of phagosome acidification / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / Nef Mediated CD8 Down-regulation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / Golgi lumen acidification / proton-transporting V-type ATPase, V0 domain / Transferrin endocytosis and recycling / extrinsic component of synaptic vesicle membrane / endosome to plasma membrane protein transport / 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 / regulation of pH / Amino acids regulate mTORC1 / proton-transporting V-type ATPase complex / osteoclast development / 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 / azurophil granule membrane / proton transmembrane transporter activity / microvillus / autophagosome membrane / ATPase activator activity / tertiary granule membrane / ficolin-1-rich granule membrane / positive regulation of Wnt signaling pathway / cilium assembly / RHOA GTPase cycle / transmembrane transporter complex / regulation of macroautophagy / ossification / specific granule membrane / enzyme regulator activity / ATP metabolic process / axon terminus / H+-transporting two-sector ATPase / ruffle / Insulin receptor recycling / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / brush border membrane / sensory perception of sound / cilium / transmembrane transport / small GTPase binding / synaptic vesicle membrane / endocytosis / phagocytic vesicle membrane / melanosome / apical part of cell / ATPase binding / signaling receptor activity / intracellular iron ion homeostasis / membrane => GO:0016020 / endosome / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / endosome membrane / early endosome / apical plasma membrane / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / Neutrophil degranulation / protein-containing complex binding / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å | ||||||||||||
Authors | Wang, R. / Li, X. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7unf.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7unf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7unf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7unf_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7unf_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7unf_validation.xml.gz | 202.5 KB | Display | |
Data in CIF | 7unf_validation.cif.gz | 321.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/7unf ftp://data.pdbj.org/pub/pdb/validation_reports/un/7unf | HTTPS FTP |
-Related structure data
Related structure data | 26623MC 7uneC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: ATP6V0A4, ATP6N1B, ATP6N2 / Production host: Homo sapiens (human) / References: UniProt: Q9HBG4 | ||||||||||||||||||||||||
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#3: Protein | Mass: 68379.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) 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) Homo sapiens (human) / References: UniProt: P21281 #5: Protein | | Mass: 28311.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5K8 #6: Protein | Mass: 26183.346 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36543 #7: Protein | Mass: 13781.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75348 #8: Protein | | Mass: 13388.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16864 #9: Protein | | Mass: 43999.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21283 #10: Protein | | Mass: 55949.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI12 #11: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61421 #12: Protein | | Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15342 #14: Protein | | Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15904 #16: Protein | Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27449 #17: Protein | | Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99437 |
-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) Homo sapiens (human) / References: UniProt: D3DUL8 |
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#13: Protein | Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) 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) Homo sapiens (human) / References: UniProt: A0A1B0GVW0 |
-Sugars , 3 types, 8 molecules
#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
#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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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 |