+Open data
-Basic information
Entry | Database: PDB / ID: 6wlw | ||||||
---|---|---|---|---|---|---|---|
Title | The Vo region of human V-ATPase in state 1 (focused refinement) | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / V-ATPase / proton pump | ||||||
Function / homology | Function and homology information proton-transporting two-sector ATPase complex / Ion channel transport / eye pigmentation / 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 / positive regulation of transforming growth factor beta1 production ...proton-transporting two-sector ATPase complex / Ion channel transport / eye pigmentation / 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 / 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 / Golgi lumen acidification / lysosomal lumen acidification / Transferrin endocytosis and recycling / clathrin-coated vesicle membrane / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / XBP1(S) activates chaperone genes / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / Amino acids regulate mTORC1 / head morphogenesis / vacuolar acidification / transmembrane transporter complex / ROS and RNS production in phagocytes / dendritic spine membrane / regulation of cellular pH / osteoclast development / azurophil granule membrane / ATPase activator activity / autophagosome membrane / regulation of MAPK cascade / tertiary granule membrane / ficolin-1-rich granule membrane / cilium assembly / positive regulation of Wnt signaling pathway / RHOA GTPase cycle / angiotensin maturation / regulation of macroautophagy / Metabolism of Angiotensinogen to Angiotensins / axon terminus / RNA endonuclease activity / Insulin receptor recycling / proton-transporting ATPase activity, rotational mechanism / receptor-mediated endocytosis / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / secretory granule membrane / transmembrane transport / synaptic vesicle membrane / small GTPase binding / phagocytic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / signaling receptor activity / 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 / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Wang, L. / Wu, H. / Fu, T.-M. | ||||||
Citation | Journal: Mol Cell / Year: 2020 Title: Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. Authors: Longfei Wang / Di Wu / Carol V Robinson / Hao Wu / Tian-Min Fu / Abstract: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton ...Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the V complex. We define ATP6AP1 as a structural hub for V complex assembly because it connects to multiple V subunits and phospholipids in the c-ring. The glycolipids and the glycosylated V subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wlw.cif.gz | 503.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wlw.ent.gz | 420.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/6wlw ftp://data.pdbj.org/pub/pdb/validation_reports/wl/6wlw | HTTPS FTP |
---|
-Related structure data
Related structure data | 21844MC 6wlzC 6wm2C 6wm3C 6wm4C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
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
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-V-type proton ATPase ... , 6 types, 14 molecules 0123456789QRSU
#1: Protein | Mass: 21418.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99437 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Protein | Mass: 15743.655 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27449 #3: Protein | | Mass: 40369.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61421 #4: Protein | | Mass: 96512.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q93050 #5: Protein | | Mass: 9380.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15342 #7: Protein | | Mass: 52067.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15904 |
-Protein , 2 types, 2 molecules TV
#6: Protein | Mass: 15435.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q6P5S7, Hydrolases; Acting on ester bonds |
---|---|
#8: Protein | Mass: 39045.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75787 |
-Sugars , 5 types, 9 molecules
#9: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
---|---|---|---|---|---|
#10: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose | ||||
#11: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #12: 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)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #19: Sugar | ChemComp-NAG / | |
-Non-polymers , 6 types, 30 molecules
#13: Chemical | ChemComp-WSS / #14: Chemical | ChemComp-PTY / #15: Chemical | ChemComp-WJS / ( | #16: Chemical | ChemComp-CLR / #17: Chemical | ChemComp-PSF / | #18: Chemical | ChemComp-WJP / | |
---|
-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: Human V-ATPase with SidK / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|