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- PDB-3nwd: Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nwd | |||||||||
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Title | Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH | |||||||||
![]() | Envelope glycoprotein B | |||||||||
![]() | VIRAL PROTEIN / Coiled-Coil / ENVELOPE GLYCOPROTEIN / MEMBRANE FUSION / Glycoprotein B / Herpesvirus 1 / HSV-1 / Membrane | |||||||||
Function / homology | ![]() host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stampfer, S.D. / Lou, H. / Cohen, G.H. / Eisenberg, R.J. / Heldwein, E.E. | |||||||||
![]() | ![]() Title: Structural basis of local, pH-dependent conformational changes in glycoprotein B from herpes simplex virus type 1. Authors: Stampfer, S.D. / Lou, H. / Cohen, G.H. / Eisenberg, R.J. / 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 | ![]() | 441.4 KB | Display | ![]() |
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PDB format | ![]() | 362.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 87.8 KB | Display | |
Data in CIF | ![]() | 115.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nw8C ![]() 3nwaSC ![]() 3nwfC 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules BACD
#1: Protein | Mass: 78797.203 Da / Num. of mol.: 4 / Fragment: Ectodomain (UNP residues 30 to 730) / Mutation: Y179S Source method: isolated from a genetically manipulated source Details: Y179S mutation Source: (gene. exp.) ![]() ![]() Strain: KOS / Gene: gB, UL27 / Plasmid: pVT-Bac / Production host: ![]() ![]() |
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-Sugars , 2 types, 11 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 87 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MRY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MRY.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-MRY / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT HSV-1 STRAIN KOS SEQUENCE IN THE UNP DATABASE CONTAINS THREE MUTATIONS RELATIVE ...AUTHORS STATE THAT HSV-1 STRAIN KOS SEQUENCE IN THE UNP DATABASE CONTAINS THREE MUTATIONS RELATIVE TO SEQUENCES OF OTHER STRAINS OF HSV-1 AND HSV-2. THEIR SEQUENCE WAS DERIVED FROM THE SEQUENCE OF HSV-1 KOS GB FROM PLASMID PKBXX (S. PERSON) AND DOES NOT CONTAIN THESE MUTATIONS. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2008 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.88026→48.5625 Å / Num. all: 111822 / Num. obs: 111383 / % possible obs: 99.6074 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.27 |
Reflection shell | Resolution: 2.88→2.98 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.04 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NWA Resolution: 2.8803→48.5625 Å / Cross valid method: THROUGHOUT / σ(F): 0.07 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.392 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8803→48.5625 Å
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Refine LS restraints |
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LS refinement shell |
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