[English] 日本語
Yorodumi- EMDB-22880: Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22880 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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 / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels ...ROS and RNS production in phagocytes / Insulin receptor recycling / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Ion channel transport / Metabolism of Angiotensinogen to Angiotensins / pH reduction / RHOA GTPase cycle / plasma membrane proton-transporting V-type ATPase complex / cellular response to increased oxygen levels / synaptic vesicle lumen acidification / 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 / proton-transporting V-type ATPase complex / cell projection organization / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / Neutrophil degranulation / autophagosome membrane / ATPase activator activity / positive regulation of Wnt signaling pathway / cilium assembly / regulation of macroautophagy / endomembrane system / ATP metabolic process / H+-transporting two-sector ATPase / transport vesicle / proton transmembrane transport / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / transmembrane transport / cilium / synaptic vesicle membrane / melanosome / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / external side of plasma membrane / axon / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) / Bovine (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||
Authors | Wang R / Li X | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Molecular basis of V-ATPase inhibition by bafilomycin A1. Authors: Rong Wang / Jin Wang / Abdirahman Hassan / Chia-Hsueh Lee / Xiao-Song Xie / Xiaochun Li / Abstract: Pharmacological inhibition of vacuolar-type H-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a ...Pharmacological inhibition of vacuolar-type H-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Although there are many V-ATPase structures reported, the molecular basis of specific inhibitors on V-ATPase remains unknown. Here, we report the cryo-EM structure of bafilomycin A1 bound intact bovine V-ATPase at an overall resolution of 3.6-Å. The structure reveals six bafilomycin A1 molecules bound to the c-ring. One bafilomycin A1 molecule engages with two c subunits and disrupts the interactions between the c-ring and subunit a, thereby preventing proton translocation. Structural and sequence analyses demonstrate that the bafilomycin A1-binding residues are conserved in yeast and mammalian species and the 7'-hydroxyl group of bafilomycin A1 acts as a unique feature recognized by subunit c. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22880.map.gz | 432.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22880-v30.xml emd-22880.xml | 27.4 KB 27.4 KB | Display Display | EMDB header |
Images | emd_22880.png | 28.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22880 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22880 | HTTPS FTP |
-Validation report
Summary document | emd_22880_validation.pdf.gz | 547.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22880_full_validation.pdf.gz | 546.9 KB | Display | |
Data in XML | emd_22880_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | emd_22880_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22880 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22880 | HTTPS FTP |
-Related structure data
Related structure data | 7khrMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22880.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bo...
+Supramolecule #1: Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bo...
+Macromolecule #1: V-type proton ATPase catalytic subunit A
+Macromolecule #2: V-type proton ATPase subunit B, brain isoform
+Macromolecule #3: V-type proton ATPase subunit C 1
+Macromolecule #4: V-type proton ATPase subunit D
+Macromolecule #5: V-type proton ATPase subunit E 1
+Macromolecule #6: V-type proton ATPase subunit F
+Macromolecule #7: V-type proton ATPase subunit G
+Macromolecule #8: V-type proton ATPase subunit H
+Macromolecule #9: V-type proton ATPase subunit a
+Macromolecule #10: V-type proton ATPase 21 kDa proteolipid subunit
+Macromolecule #11: V-type proton ATPase subunit d 1
+Macromolecule #12: V-type proton ATPase subunit e 2
+Macromolecule #13: V-type proton ATPase subunit S1
+Macromolecule #14: Renin receptor
+Macromolecule #15: V-type proton ATPase 16 kDa proteolipid subunit
+Macromolecule #16: Ribonuclease kappa
+Macromolecule #19: MAGNESIUM ION
+Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #21: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-t...
+Macromolecule #22: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
+Macromolecule #23: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #24: OLEIC ACID
+Macromolecule #25: (5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S...
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26530 |
---|---|
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |