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- PDB-7zio: JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zio | ||||||
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Title | JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aromatic linker) | ||||||
![]() | Major capsid protein VP1 | ||||||
![]() | VIRAL PROTEIN / Complex / Sialic acid / Capsid protein | ||||||
Function / homology | ![]() T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Freytag, J. / Mueller, J.C. / Stehle, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis of Homo- and Heteromultivalent Fucosylated and Sialylated Oligosaccharide Conjugates via Preactivated N -Methyloxyamine Precision Macromolecules and Their Binding to Polyomavirus Capsid Proteins. Authors: Konietzny, P.B. / Freytag, J. / Feldhof, M.I. / Muller, J.C. / Ohl, D. / Stehle, T. / Hartmann, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 663.4 KB | Display | ![]() |
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Full document | ![]() | 669.3 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 48.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zilC ![]() 7zimC ![]() 7zinC ![]() 7zipC ![]() 7ziqC ![]() 3nxdS S: Starting model for refinement 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
-Protein , 1 types, 5 molecules AAABBBCCCDDDEEE
#1: Protein | Mass: 30075.861 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose | |
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-Non-polymers , 5 types, 1537 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-CL / | #8: 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: 2.94 Å3/Da / Density % sol: 58.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.165 Å / Num. obs: 173290 / % possible obs: 99.2 % / Redundancy: 5.07 % / CC1/2: 0.99 / Rrim(I) all: 0.18 / Net I/σ(I): 8.31 |
Reflection shell | Resolution: 1.75→1.86 Å / Num. unique obs: 27318 / CC1/2: 0.58 / Rrim(I) all: 1.27 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NXD Resolution: 1.751→45.165 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.075 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.101 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.461 Å2
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Refinement step | Cycle: LAST / Resolution: 1.751→45.165 Å
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Refine LS restraints |
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LS refinement shell |
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