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- PDB-4xi5: gHgL of varicella-zoster virus in complex with human neutralizing... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xi5 | |||||||||
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Title | gHgL of varicella-zoster virus in complex with human neutralizing antibodies | |||||||||
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![]() | Viral Protein/Immune System / complex / neutralization epitope / Viral Protein-Immune System complex | |||||||||
Function / homology | ![]() host cell endosome membrane / host cell Golgi apparatus / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xing, Y. | |||||||||
![]() | ![]() Title: A site of varicella-zoster virus vulnerability identified by structural studies of neutralizing antibodies bound to the glycoprotein complex gHgL. Authors: Xing, Y. / Oliver, S.L. / Nguyen, T. / Ciferri, C. / Nandi, A. / Hickman, J. / Giovani, C. / Yang, E. / Palladino, G. / Grose, C. / Uematsu, Y. / Lilja, A.E. / Arvin, A.M. / Carfi, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.8 KB | Display | ![]() |
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PDB format | ![]() | 204.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xhjSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Envelope glycoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 92763.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 15197.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 23172.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#4: Antibody | Mass: 30198.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#6: Sugar |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES pH 6.0 and 4% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8852→200 Å / Num. obs: 23170 / % possible obs: 99.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 3.8852→3.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4XHJ Resolution: 3.9→37.322 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→37.322 Å
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Refine LS restraints |
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LS refinement shell |
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