+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-0646 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1 | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Proton pump / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly ...vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / P-type proton-exporting transporter activity / pexophagy / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / protein targeting to vacuole / vacuole organization / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-4-phosphate binding / plant-type vacuole / vacuolar acidification / fungal-type vacuole membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / endomembrane system / ATP metabolic process / H+-transporting two-sector ATPase / Neutrophil degranulation / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / cell periphery / transmembrane transport / intracellular calcium ion homeostasis / cytoplasmic stress granule / endocytosis / late endosome / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / endosome membrane / membrane raft / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
![]() | Vasanthakumar T / Bueler SA / Wu D / Beilsten-Edmands V / Robinson CV / Rubinstein JL | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural comparison of the vacuolar and Golgi V-ATPases from . Authors: Thamiya Vasanthakumar / Stephanie A Bueler / Di Wu / Victoria Beilsten-Edmands / Carol V Robinson / John L Rubinstein / ![]() ![]() Abstract: Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal ...Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V complexes containing Stv1p could be readily purified without attached V regions. We used this effect to determine structures of the membrane-embedded V region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 31 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 28.8 KB 28.8 KB | Display Display | ![]() |
Images | ![]() | 29.2 KB | ||
Filedesc metadata | ![]() | 8.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o7vMC ![]() 0644C ![]() 0645C ![]() 0647C ![]() 0648C ![]() 6o7tC ![]() 6o7uC ![]() 6o7wC ![]() 6o7xC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1
+Supramolecule #1: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1
+Macromolecule #1: V-type proton ATPase subunit D
+Macromolecule #2: V-type proton ATPase subunit F
+Macromolecule #3: Vacuolar ATP synthase catalytic subunit A
+Macromolecule #4: V-type proton ATPase subunit B
+Macromolecule #5: V-type proton ATPase subunit G
+Macromolecule #6: V-type proton ATPase subunit E
+Macromolecule #7: V-type proton ATPase subunit H
+Macromolecule #8: V-type proton ATPase subunit C
+Macromolecule #9: V-type proton ATPase subunit a, Golgi isoform
+Macromolecule #10: V0 assembly protein 1
+Macromolecule #11: V-type proton ATPase subunit c''
+Macromolecule #12: V-type proton ATPase subunit d
+Macromolecule #13: V-type proton ATPase subunit c
+Macromolecule #14: V-type proton ATPase subunit c'
+Macromolecule #15: V-type proton ATPase subunit e
+Macromolecule #16: Putative protein YPR170W-B
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-
Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER / Details: Ab initio |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25045 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |