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Yorodumi- PDB-3fus: Improved Structure of the Unliganded Simian Immunodeficiency Viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fus | |||||||||
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Title | Improved Structure of the Unliganded Simian Immunodeficiency Virus gp120 Core | |||||||||
Components | EXTERIOR MEMBRANE GLYCOPROTEIN GP120 | |||||||||
Keywords | VIRAL PROTEIN / SIV / AIDS / gp120 / structural refinement / normal mode / Apoptosis / Cell membrane / Envelope protein / Fusion protein / Host-virus interaction / Membrane / Transmembrane / Virion | |||||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Simian immunodeficiency virus | |||||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 4 Å | |||||||||
Authors | Chen, X. / Poon, B. / Wang, Q. / Ma, J. | |||||||||
Citation | Journal: Structure / Year: 2005 Title: Determining the structure of an unliganded and fully glycosylated SIV gp120 envelope glycoprotein. Authors: Chen, B. / Vogan, E.M. / Gong, H. / Skehel, J.J. / Wiley, D.C. / Harrison, S.C. | |||||||||
History |
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Remark 0 | THIS ENTRY 3FUS REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2BF1SF) ...THIS ENTRY 3FUS REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2BF1SF) DETERMINED BY AUTHORS OF THE PDB ENTRY 2BF1:B.CHEN,E.M.VOGAN,H.GONG,J.J.SKEHEL,D.C.WILEY,S.C.HARRISON |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fus.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fus.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fus_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 3fus_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 3fus_validation.xml.gz | 24 KB | Display | |
Data in CIF | 3fus_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fus ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fus | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | GP120 CORE, RESIDUES 66-109, 209-311, 342-502 |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36833.723 Da / Num. of mol.: 1 / Fragment: GP120 CORE, RESIDUES 66-109, 209-311, 342-502 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Gene: env / Plasmid: PSIVGP120CORE / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI5 / References: UniProt: Q07374 |
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-Sugars , 11 types, 13 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||||||||||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: 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 #8: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Polysaccharide | beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-beta-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 #10: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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 #11: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #12: Sugar | |
-Details
Has protein modification | Y |
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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: 4.66 Å3/Da / Density % sol: 73.62 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2BF1. |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MIRAS / Resolution: 4→25.58 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.883 / SU B: 244.543 / SU ML: 1.516 / Cross valid method: THROUGHOUT / ESU R Free: 1.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 2.8 Å / VDW probe radii: 3 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 131.846 Å2
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Refinement step | Cycle: LAST / Resolution: 4→25.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4→4.101 Å / Total num. of bins used: 20
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