+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27984 | |||||||||
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Title | Yeast VO in complex with Vma12-22p | |||||||||
Map data | ||||||||||
Sample |
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Keywords | V-type / ATPase / assembly / proton / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Vma12-Vma22 assembly complex / vacuolar proton-transporting V-type ATPase complex assembly / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process ...Vma12-Vma22 assembly complex / vacuolar proton-transporting V-type ATPase complex assembly / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / protein targeting to vacuole / vacuole organization / proton-transporting V-type ATPase complex / fungal-type vacuole / cellular hyperosmotic response / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-3,5-bisphosphate binding / vacuolar acidification / fungal-type vacuole membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / Neutrophil degranulation / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / unfolded protein binding / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / endoplasmic reticulum membrane / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Wang H / Bueler SA / Rubinstein JL | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structural basis of V-ATPase V region assembly by Vma12p, 21p, and 22p. Authors: Hanlin Wang / Stephanie A Bueler / John L Rubinstein / Abstract: Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a ...Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a soluble catalytic V region and a membrane-embedded proton-translocating V region. V is assembled in the endoplasmic reticulum (ER) membrane, and V is assembled in the cytosol. However, V binds V only after V is transported to the Golgi membrane, thereby preventing acidification of the ER. We isolated V complexes and subcomplexes from bound to V-ATPase assembly factors Vma12p, Vma21p, and Vma22p. Electron cryomicroscopy shows how the Vma12-22p complex recruits subunits a, e, and f to the rotor ring of V while blocking premature binding of V. Vma21p, which contains an ER-retrieval motif, binds the V:Vma12-22p complex, "mature" V, and a complex that appears to contain a ring of loosely packed rotor subunits and the proteins YAR027W and YAR028W. The structures suggest that Vma21p binds assembly intermediates that contain a rotor ring and that activation of proton pumping following assembly of V with V removes Vma21p, allowing V-ATPase to remain in the Golgi. Together, these structures show how Vma12-22p and Vma21p function in V-ATPase assembly and quality control, ensuring the enzyme acidifies only its intended cellular targets. #1: Journal: Biorxiv / Year: 2022 Title: Structural basis of V-ATPase V0 region assembly by Vma12p, 21p, and 22p Authors: Wang H / Bueler SA / Rubinstein JL | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27984.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-27984-v30.xml emd-27984.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
Images | emd_27984.png | 63.8 KB | ||
Filedesc metadata | emd-27984.cif.gz | 7 KB | ||
Others | emd_27984_half_map_1.map.gz emd_27984_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27984 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27984 | HTTPS FTP |
-Validation report
Summary document | emd_27984_validation.pdf.gz | 850.6 KB | Display | EMDB validaton report |
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Full document | emd_27984_full_validation.pdf.gz | 850.2 KB | Display | |
Data in XML | emd_27984_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_27984_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27984 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27984 | HTTPS FTP |
-Related structure data
Related structure data | 8easMC 8eatC 8eauC 8eavC 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 |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27984.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27984_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27984_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast Vo in complex with Vma12-22p
+Supramolecule #1: Yeast Vo in complex with Vma12-22p
+Macromolecule #1: Vacuolar ATPase assembly protein VMA22
+Macromolecule #2: V-type proton ATPase assembly factor Vma12p
+Macromolecule #3: V-type proton ATPase subunit F
+Macromolecule #4: V-type proton ATPase subunit a, vacuolar isoform
+Macromolecule #5: V0 assembly protein 1
+Macromolecule #6: V-type proton ATPase subunit c''
+Macromolecule #7: V-type proton ATPase subunit d
+Macromolecule #8: V-type proton ATPase subunit e
+Macromolecule #9: Yeast V-ATPase subunit f
+Macromolecule #10: V-type proton ATPase subunit c
+Macromolecule #11: V-type proton ATPase subunit c'
-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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Grid | Model: Homemade / Material: COPPER/RHODIUM |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 308537 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |