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- PDB-8igv: Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8igv | |||||||||||||||
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Title | Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP-Pi)1cat(ADP)2cat,2non-cat | |||||||||||||||
![]() | (V-type sodium ATPase ...) x 2 | |||||||||||||||
![]() | MOTOR PROTEIN / Computational Design / Rotary Molecular Motor / Complex | |||||||||||||||
Function / homology | ![]() Na+-transporting two-sector ATPase / sodium-transporting ATP synthase activity, rotational mechanism / sodium-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...Na+-transporting two-sector ATPase / sodium-transporting ATP synthase activity, rotational mechanism / sodium-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / ATP binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Kosugi, T. / Tanabe, M. / Koga, N. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites. Authors: Kosugi, T. / Iida, T. / Tanabe, M. / Iino, R. / Koga, N. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 638.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 110.3 KB | Display | |
Data in CIF | ![]() | 147.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iguC ![]() 8igwC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-V-type sodium ATPase ... , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 66059.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 9790 / Gene: ntpA, EHR_08260 / Production host: ![]() ![]() References: UniProt: Q08636, Na+-transporting two-sector ATPase #2: Protein | Mass: 51017.219 Da / Num. of mol.: 3 Mutation: S151G, G152P, S153P, L155A, P156G, G157K, K158S, E159A, T248E, Q339S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 9790 / Gene: ntpB, EHR_08265 / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 128 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl (pH 8.5), 24% PEG 3350, 0.2 M Ammonium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→48.38 Å / Num. obs: 63835 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 55.73 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.087 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.15→3.23 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2 / Num. unique obs: 4482 / CC1/2: 0.569 / Rpim(I) all: 0.49 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→48.38 Å
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Refine LS restraints |
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LS refinement shell |
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