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Yorodumi- PDB-6bm8: Crystal structure of glycoprotein B from Herpes Simplex Virus type I -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bm8 | ||||||||||||
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Title | Crystal structure of glycoprotein B from Herpes Simplex Virus type I | ||||||||||||
Components | Envelope glycoprotein B | ||||||||||||
Keywords | VIRAL PROTEIN / fusogen / bitopic membrane protein | ||||||||||||
Function / homology | Function and homology information 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 / membrane Similarity search - Function | ||||||||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1 Å | ||||||||||||
Authors | Cooper, R.S. / Heldwein, E.E. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bm8.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bm8.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/6bm8 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bm8 | HTTPS FTP |
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-Related structure data
Related structure data | 5v2sC 2gumS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 93528.438 Da / Num. of mol.: 1 / Fragment: residues 72-904 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Gene: UL27, gB, HHV1gp041 / Plasmid: pFastBac / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A1Z0P7, UniProt: P10211*PLUS |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.2 Å3/Da / Density % sol: 82.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 4000, 0.1 M Tris HCl pH 7.5, 0.1 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.99→101.87 Å / Num. obs: 19003 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 164.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.072 / Rrim(I) all: 0.131 / Net I/σ(I): 7 / Num. measured all: 62145 / Scaling rejects: 6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GUM Resolution: 4.1→101.87 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 318.74 Å2 / Biso mean: 190.5642 Å2 / Biso min: 106.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.1→101.87 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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