+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26334 | |||||||||
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Title | Human V-ATPase in state 2 with SidK and mEAK-7 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | V-ATPase / mEAK-7 / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information : / proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / eye pigmentation / positive regulation of protein localization to lysosome / central nervous system maturation / intracellular pH reduction / plasma membrane proton-transporting V-type ATPase complex / transporter activator activity ...: / proton-transporting two-sector ATPase complex / Blockage of phagosome acidification / Ion channel transport / eye pigmentation / positive regulation of protein localization to lysosome / central nervous system maturation / intracellular pH reduction / plasma membrane proton-transporting V-type ATPase complex / transporter activator activity / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / Nef Mediated CD8 Down-regulation / positive regulation of transforming growth factor beta1 production / ATPase-coupled ion transmembrane transporter activity / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / Golgi lumen acidification / Transferrin endocytosis and recycling / lysosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / XBP1(S) activates chaperone genes / vacuolar proton-transporting V-type ATPase complex / Amino acids regulate mTORC1 / head morphogenesis / vacuolar acidification / protein localization to cilium / transmembrane transporter complex / ROS and RNS production in phagocytes / Nef Mediated CD4 Down-regulation / dendritic spine membrane / regulation of cellular pH / osteoclast development / azurophil granule membrane / TOR signaling / ATPase activator activity / autophagosome membrane / regulation of MAPK cascade / microvillus / tertiary granule membrane / ficolin-1-rich granule membrane / proton transmembrane transporter activity / cilium assembly / positive regulation of Wnt signaling pathway / RHOA GTPase cycle / angiotensin maturation / regulation of macroautophagy / response to amino acid / Metabolism of Angiotensinogen to Angiotensins / enzyme regulator activity / specific granule membrane / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / regulation of cell migration / RNA endonuclease activity / ruffle / Insulin receptor recycling / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / response to nutrient levels / receptor-mediated endocytosis / secretory granule membrane / secretory granule / response to insulin / cilium / transmembrane transport / synaptic vesicle membrane / small GTPase binding / endocytosis / phagocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / presynapse / apical part of cell / signaling receptor activity / regulation of cell population proliferation / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / lysosome / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Legionella pneumophila (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang L / Fu TM | |||||||||
Funding support | 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Identification of mEAK-7 as a human V-ATPase regulator via cryo-EM data mining. Authors: Longfei Wang / Di Wu / Carol V Robinson / Tian-Min Fu / Abstract: Vacuolar-type adenosine triphosphatases (V-ATPases) not only function as rotary proton pumps in cellular organelles but also serve as signaling hubs. To identify the endogenous binding partners of V- ...Vacuolar-type adenosine triphosphatases (V-ATPases) not only function as rotary proton pumps in cellular organelles but also serve as signaling hubs. To identify the endogenous binding partners of V-ATPase, we collected a large dataset of human V-ATPases and did extensive classification and focused refinement of human V-ATPases. Unexpectedly, about 17% of particles in state 2 of human V-ATPases display additional density with an overall resolution of 3.3 Å. Structural analysis combined with artificial intelligence modeling enables us to identify this additional density as mEAK-7, a protein involved in mechanistic target of rapamycin (mTOR) signaling in mammals. Our structure shows that mEAK-7 interacts with subunits A, B, D, and E of V-ATPases in state 2. Thus, we propose that mEAK-7 may regulate V-ATPase function through binding to V-ATPases in state 2 as well as mediate mTOR signaling. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26334.map.gz | 168.2 MB | EMDB map data format | |
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Header (meta data) | emd-26334-v30.xml emd-26334.xml | 38 KB 38 KB | Display Display | EMDB header |
Images | emd_26334.png | 156.5 KB | ||
Others | emd_26334_additional_1.map.gz emd_26334_additional_2.map.gz emd_26334_half_map_1.map.gz emd_26334_half_map_2.map.gz | 168.2 MB 158.8 MB 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26334 | HTTPS FTP |
-Related structure data
Related structure data | 7u4tMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11132 (Title: Cryo-EM structures of human V-ATPase / Data size: 8.4 TB Data #1: Unaligned multi frame micrographs of human V-ATPase in complex with SidK [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26334.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Local refinement map of mEAK-7 and nearby subunits
File | emd_26334_additional_1.map | ||||||||||||
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Annotation | Local refinement map of mEAK-7 and nearby subunits | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite map
File | emd_26334_additional_2.map | ||||||||||||
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Annotation | Composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26334_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26334_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : V-ATPase with SidK and mEAK-7
+Supramolecule #1: V-ATPase with SidK and mEAK-7
+Macromolecule #1: V-type proton ATPase 116 kDa subunit a isoform 1
+Macromolecule #2: V-type proton ATPase subunit C 1
+Macromolecule #3: V-type proton ATPase subunit E 1
+Macromolecule #4: V-type proton ATPase subunit G 1
+Macromolecule #5: V-type proton ATPase subunit e 1
+Macromolecule #6: Ribonuclease kappa
+Macromolecule #7: V-type proton ATPase subunit S1
+Macromolecule #8: Renin receptor
+Macromolecule #9: V-type proton ATPase 21 kDa proteolipid subunit
+Macromolecule #10: V-type proton ATPase 16 kDa proteolipid subunit
+Macromolecule #11: V-type proton ATPase subunit d 1
+Macromolecule #12: V-type proton ATPase catalytic subunit A
+Macromolecule #13: V-type proton ATPase subunit B, brain isoform
+Macromolecule #14: SidK
+Macromolecule #15: V-type proton ATPase subunit D
+Macromolecule #16: V-type proton ATPase subunit F
+Macromolecule #17: V-type proton ATPase subunit H
+Macromolecule #18: MTOR-associated protein MEAK7
+Macromolecule #19: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170000 |