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Yorodumi- PDB-3fus: Improved Structure of the Unliganded Simian Immunodeficiency Viru... -
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Open data
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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 informationmembrane fusion involved in viral entry into host cell / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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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 |
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Links
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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 |
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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 |
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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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About Yorodumi



Simian immunodeficiency virus
X-RAY DIFFRACTION
Citation










PDBj



Trichoplusia ni (cabbage looper)