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Open data
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Basic information
Entry | Database: PDB / ID: 4ix9 | ||||||
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Title | Crystal structure of subunit F of V-ATPase from S. cerevisiae | ||||||
![]() | V-type proton ATPase subunit F | ||||||
![]() | HYDROLASE / V-ATPase / stalk subunit / subunit F / Rossmann fold / Regulatory / coupling | ||||||
Function / homology | ![]() Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / Golgi membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Basak, S. / Balakrishna, A.M. / Manimekalai, M.S.S. / Gruber, G. | ||||||
![]() | ![]() Title: Crystal and NMR structures give insights into the role and dynamics of subunit F of the eukaryotic V-ATPase from Saccharomyces cerevisiae Authors: Basak, S. / Lim, J. / Manimekalai, M.S.S. / Balakrishna, A.M. / Gruber, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.9 KB | Display | ![]() |
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Full document | ![]() | 497 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 10760.775 Da / Num. of mol.: 4 Fragment: Coupling and Regulatory Subunit F, UNP residues 1-94 Mutation: I69M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: VMA7, YGR020C / Plasmid: pET9d / Production host: ![]() ![]() References: UniProt: P39111, H+-transporting two-sector ATPase #2: Chemical | ChemComp-TRS / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2012 Details: Vertically Collimating Premirror, Toroidal Focusing Mirror | ||||||||||||
Radiation | Monochromator: Double Crystal Si(111) Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.33→50 Å / Num. all: 17114 / Num. obs: 17018 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.8 | ||||||||||||
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1612 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.034 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→26.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.328→2.389 Å / Total num. of bins used: 20
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