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- PDB-5v2s: Crystal structure of glycoprotein B from Herpes Simplex Virus type I -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v2s | ||||||||||||
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Title | Crystal structure of glycoprotein B from Herpes Simplex Virus type I | ||||||||||||
![]() | Envelope glycoprotein B | ||||||||||||
![]() | VIRAL PROTEIN / fusogen / bitopic membrane protein | ||||||||||||
Function / homology | ![]() host cell Golgi membrane / host cell endosome membrane / host cell endosome / host cell Golgi apparatus / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Cooper, R.S. / Heldwein, E.E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for membrane anchoring and fusion regulation of the herpes simplex virus fusogen gB. Authors: Cooper, R.S. / Georgieva, E.R. / Borbat, P.P. / Freed, J.H. / Heldwein, E.E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.5 KB | Display | ![]() |
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PDB format | ![]() | 122.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.2 KB | Display | ![]() |
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Full document | ![]() | 1013.1 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 35.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bm8C ![]() 2gumS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Details | Trimer as determined by gel filtration |
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Components
#1: Protein | Mass: 94501.469 Da / Num. of mol.: 1 / Fragment: residues 72-904 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: UL27, HHV1gp041 / Plasmid: pFastBac / Cell line (production host): SF9 / Production host: ![]() ![]() | ||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 73.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 16% PEG 3350, 0.1 M Na Hepes pH 7.2, 0.15 M Na formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→108.232 Å / Num. obs: 21107 / % possible obs: 99.7 % / Redundancy: 8.4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.3297 / Rpim(I) all: 0.1196 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.6→3.729 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.833 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 2070 / CC1/2: 0.61 / Rpim(I) all: 0.6654 / % possible all: 99.76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GUM Resolution: 3.6→108.232 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.08 / 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: 3.6→108.232 Å
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Refine LS restraints |
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