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Yorodumi- PDB-7zim: JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zim | ||||||
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Title | JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aromatic linker) | ||||||
Components | Major capsid protein VP1 | ||||||
Keywords | VIRAL PROTEIN / Complex / Sialic acid / Capsid protein | ||||||
Function / homology | Function and homology information 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 | JC polyomavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Freytag, J. / Mueller, J.C. / Stehle, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Biomacromolecules / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zim.cif.gz | 312.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zim.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7zim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/7zim ftp://data.pdbj.org/pub/pdb/validation_reports/zi/7zim | HTTPS FTP |
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-Related structure data
Related structure data | 7zilC 7zinC 7zioC 7zipC 7ziqC 3nxdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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.) JC polyomavirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03089 #2: Polysaccharide | Source method: isolated from a genetically manipulated source Details: oligosaccharide / References: BIRD: PRD_002415 #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source Details: oligosaccharide / References: BIRD: PRD_002415 #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.66 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99 Å |
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: 1.55→44.8 Å / Num. obs: 248912 / % possible obs: 95.9 % / Redundancy: 4.74 % / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 10.61 |
Reflection shell | Resolution: 1.55→1.64 Å / Num. unique obs: 39897 / CC1/2: 0.49 / Rrim(I) all: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NXD Resolution: 1.55→44.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.067 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: 18.833 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→44.8 Å
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Refine LS restraints |
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LS refinement shell |
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