+Open data
-Basic information
Entry | Database: PDB / ID: 3vie | ||||||
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Title | HIV-gp41 fusion inhibitor Sifuvirtide | ||||||
Components |
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Keywords | VIRAL PROTEIN/ANTIVIRAL PROTEIN / 6-helix bundle / membrane fusion inhibition / HIV / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yao, X. / Waltersperger, S. / Wang, M.T. / Cui, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Broad antiviral activity and crystal structure of HIV-1 fusion inhibitor sifuvirtide Authors: Yao, X. / Chong, H. / Zhang, C. / Waltersperger, S. / Wang, M. / Cui, S. / He, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vie.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vie.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/3vie ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3vie | HTTPS FTP |
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-Related structure data
Related structure data | 1envS 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/peptide | Mass: 4152.843 Da / Num. of mol.: 3 / Fragment: NHR domain, UNP residues 554-589 / Source method: obtained synthetically / Details: NHR 35-70 sequence occurs naturally in HIV-1 / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YP39, UniProt: P04578*PLUS #2: Protein/peptide | Mass: 4717.020 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: Sequence of Sifuvirtide has been designed based on sequence of HIV-1 gp41 CHR #3: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris HCl, 10% w/v PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2011 |
Radiation | Monochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.701→44.391 Å / Num. obs: 24817 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.18 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 18.53 |
Reflection shell | Resolution: 1.701→1.8 Å / Redundancy: 1.24 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.51 / % possible all: 63.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ENV Resolution: 1.8→34.936 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.25 / σ(F): 0.81 / Phase error: 22.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.439 Å2 / ksol: 0.463 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.7 Å2 / Biso mean: 31.7329 Å2 / Biso min: 12.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.936 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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