+Open data
-Basic information
Entry | Database: PDB / ID: 3vtq | ||||||
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Title | Novel HIV fusion inhibitor | ||||||
Components |
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Keywords | VIRAL PROTEIN/ANTIVIRAL PROTEIN / 6-helix bundle / coiled-coil / membrane / fusion inhibitor / M-T hook / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information 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 / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...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 / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Yao, X. / Waltersperger, S. / Wang, M. / Cui, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of a novel HIV fusion inhibitor Authors: Yao, X. / Waltersperger, S. / Wang, M. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vtq.cif.gz | 104.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vtq.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vtq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/3vtq ftp://data.pdbj.org/pub/pdb/validation_reports/vt/3vtq | HTTPS FTP |
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-Related structure data
Related structure data | 3vieS 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: 4150.851 Da / Num. of mol.: 3 / Fragment: gp41, UNP RESIDUES 554-589 / Source method: obtained synthetically / Details: NHR 35-70 sequence occurs naturally in HIV-1 virus / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YP39 #2: Protein/peptide | Mass: 4776.207 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: THE SEQUENCE HAS BEEN DESIGNED #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: 2.06 Å3/Da / Density % sol: 40.33 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.14M calcium chloride, 0.1M sodium acetate, 18 %(v/v) isopropanol, pH 4.6, 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: May 21, 2012 |
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: 1.53→36.088 Å / Num. obs: 34063 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.33 % / Rmerge(I) obs: 0.036 / Rsym value: 0.037 / Net I/σ(I): 17.37 |
Reflection shell | Resolution: 1.53→1.62 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.23 / Num. unique all: 10256 / Rsym value: 0.463 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VIE Resolution: 1.53→36.088 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 20.53 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.989 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.53→36.088 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: 12
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