[English] 日本語
Yorodumi- PDB-7khr: Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7khr | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain | ||||||
Components |
| ||||||
Keywords | PROTON TRANSPORT / bafilomycin A1 | ||||||
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) | ||||||
Method | ELECTRON MICROSCOPY / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7khr.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7khr.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7khr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7khr_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7khr_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7khr_validation.xml.gz | 203.3 KB | Display | |
Data in CIF | 7khr_validation.cif.gz | 311.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/7khr ftp://data.pdbj.org/pub/pdb/validation_reports/kh/7khr | HTTPS FTP |
-Related structure data
Related structure data | 22880MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-V-type proton ATPase ... , 14 types, 30 molecules ABCDEFGHIJKLMNOPabdescgklmnopq
#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 #2: Protein | Mass: 56637.555 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31408 #3: Protein | | Mass: 44042.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P21282 #4: Protein | | Mass: 28297.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A0A3Q1M4W9 #5: Protein | Mass: 26178.371 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P11019 #6: Protein | | Mass: 13417.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28029 #7: Protein | Mass: 13588.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q0VCV6 #8: Protein | | Mass: 54155.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1MZL6 #9: Protein | | Mass: 96431.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1MJV0 #10: Protein | | Mass: 21530.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TA24 #11: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61420 #12: Protein | | Mass: 9188.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2KIB5 #13: Protein | | Mass: 51818.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P40682 #15: Protein | Mass: 15727.726 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23956 |
---|
-Protein , 2 types, 2 molecules rf
#14: Protein | Mass: 39529.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81134 |
---|---|
#16: Protein | Mass: 11030.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: Q3ZC23, Hydrolases; Acting on ester bonds |
-Sugars , 3 types, 9 molecules
#17: Polysaccharide | alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D- ...alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
---|---|
#18: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose |
#23: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 18 molecules
#19: Chemical | ChemComp-MG / | ||||
---|---|---|---|---|---|
#20: Chemical | ChemComp-ADP / | ||||
#21: Chemical | ChemComp-WJP / | ||||
#22: Chemical | ChemComp-POV / ( #24: Chemical | ChemComp-OLA / | #25: Chemical | ChemComp-WEV / ( |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL |
---|---|
Source (natural) | Organism: Bos taurus (cattle) |
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 |
---|---|
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 |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
---|---|
3D reconstruction | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26530 / Symmetry type: POINT |