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Yorodumi- PDB-7une: The V1 region of bovine V-ATPase in complex with human mEAK7 (foc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7une | ||||||||||||
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Title | The V1 region of bovine V-ATPase in complex with human mEAK7 (focused refinement) | ||||||||||||
Components |
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Keywords | PROTON TRANSPORT / mTOR signaling | ||||||||||||
Function / homology | Function and homology information ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / pH reduction / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain ...ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / pH reduction / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / cell projection organization / vacuolar acidification / Neutrophil degranulation / H+-transporting two-sector ATPase / ATP metabolic process / transport vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / cilium / synaptic vesicle membrane / melanosome / intracellular iron ion homeostasis / lysosome / endosome / apical plasma membrane / lysosomal membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 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 | 7une.cif.gz | 787.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7une.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7une.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7une_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7une_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7une_validation.xml.gz | 127.7 KB | Display | |
Data in CIF | 7une_validation.cif.gz | 198.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/7une ftp://data.pdbj.org/pub/pdb/validation_reports/un/7une | HTTPS FTP |
-Related structure data
Related structure data | 26622MC 7unfC 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
-Protein , 2 types, 4 molecules LMNU
#1: Protein | Mass: 68420.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: P31404, H+-transporting two-sector ATPase #3: Protein | | Mass: 51982.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1609, hCG_39793 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DUL8 |
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-V-type proton ATPase subunit ... , 4 types, 10 molecules DdbcQOPgef
#2: Protein | Mass: 28297.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A0A3Q1M4W9 | ||||
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#4: Protein | Mass: 26178.371 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P11019 #5: Protein | Mass: 56637.555 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31408 #6: Protein | Mass: 13588.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q0VCV6 |
-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: Cryo-EM structure of the V1 region of bovine V-ATPase in complex with human mEAK7 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||
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: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13841 / Symmetry type: POINT |