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Yorodumi- PDB-5h0n: Crystal structure of HIV-1 fusion inhibitor MT-WQ-IDL bound to gp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h0n | ||||||
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Title | Crystal structure of HIV-1 fusion inhibitor MT-WQ-IDL bound to gp41 NHR | ||||||
Components |
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Keywords | VIRAL PROTEIN/VIRAL PROTEIN INHIBITOR / MT-WQ-IDL / HIV-1 / fusion inhibitor / VIRAL PROTEIN-VIRAL PROTEIN INHIBITOR 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zhu, Y. / Ye, S. / Zhang, R. | ||||||
Citation | Journal: J. Virol. / Year: 2017 Title: Creating an Artificial Tail Anchor as a Novel Strategy To Enhance the Potency of Peptide-Based HIV Fusion Inhibitors Authors: Su, S. / Zhu, Y. / Ye, S. / Qi, Q. / Xia, S. / Ma, Z. / Yu, F. / Wang, Q. / Zhang, R. / Jiang, S. / Lu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h0n.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h0n.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/5h0n ftp://data.pdbj.org/pub/pdb/validation_reports/h0/5h0n | HTTPS FTP |
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-Related structure data
Related structure data | 5cmzS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5252.146 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS #2: Protein/peptide | Mass: 3931.463 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 #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: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion Details: 0.2 M Zinc Acetate, 0.1 M Imidazole: HCl pH 8.0, 20% (v/v) 1,4-Butanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→39.6 Å / Num. obs: 12009 / % possible obs: 84.6 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.8→2.85 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CMZ Resolution: 2.8→39.6 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.6 Å
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Refine LS restraints |
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LS refinement shell |
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