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Yorodumi- PDB-8aic: X-ray structure of the receptor binding domain of Env glycoprotei... -
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-Basic information
Entry | Database: PDB / ID: 8aic | ||||||
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Title | X-ray structure of the receptor binding domain of Env glycoprotein of Simian Foamy virus | ||||||
Components | Envelope glycoprotein gp130 | ||||||
Keywords | VIRAL PROTEIN / Receptor binding domain | ||||||
Function / homology | Foamy virus envelope protein / Foamy virus envelope protein / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane / Envelope glycoprotein gp130 Function and homology information | ||||||
Biological species | Simian foamy virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Backovic, M. / Fernandez, I. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells. Authors: Fernandez, I. / Dynesen, L.T. / Coquin, Y. / Pederzoli, R. / Brun, D. / Haouz, A. / Gessain, A. / Rey, F.A. / Buseyne, F. / Backovic, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aic.cif.gz | 374.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aic.ent.gz | 260.5 KB | Display | PDB format |
PDBx/mmJSON format | 8aic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aic_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 8aic_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 8aic_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 8aic_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/8aic ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8aic | HTTPS FTP |
-Related structure data
Related structure data | 8aezC 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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2 |
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Unit cell |
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-Components
-Protein / Non-polymers , 2 types, 109 molecules AB
#1: Protein | Mass: 40288.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian foamy virus / Gene: env / Variant: BAK74 / Cell line (production host): 2 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Scneider / References: UniProt: K7YEW5 #7: Water | ChemComp-HOH / | |
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-Sugars , 5 types, 13 molecules
#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: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]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 #5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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 #6: Sugar | |
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-Details
Has ligand of interest | N |
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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: 5.25 Å3/Da / Density % sol: 76.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium tartarate, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.73 Å / Num. obs: 40619 / % possible obs: 99.58 % / Redundancy: 21.6 % / Biso Wilson estimate: 70.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.04364 / Net I/σ(I): 13.35 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.705 / Num. unique obs: 4041 / CC1/2: 0.689 / Rpim(I) all: 0.3719 / % possible all: 99.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Related deposition D_1292124233 Resolution: 2.8→46.73 Å / SU ML: 0.4391 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9352 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→46.73 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.3339561032 Å / Origin y: 43.2539780996 Å / Origin z: 29.6017111713 Å
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Refinement TLS group | Selection details: all |