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Yorodumi- PDB-5cmu: Artificial HIV fusion inhibitor AP1 fused to the C-terminus of gp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cmu | ||||||
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Title | Artificial HIV fusion inhibitor AP1 fused to the C-terminus of gp41 NHR | ||||||
Components | Envelope glycoprotein,AP1 | ||||||
Keywords | VIRAL PROTEIN / Enfuvirtide / HIV fusion inhibitor / AP1 / gp41 / 6-HB | ||||||
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 / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.113 Å | ||||||
Authors | Zhu, Y. / Ye, S. / Zhang, R. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy. Authors: Zhu, X. / Zhu, Y. / Ye, S. / Wang, Q. / Xu, W. / Su, S. / Sun, Z. / Yu, F. / Liu, Q. / Wang, C. / Zhang, T. / Zhang, Z. / Zhang, X. / Xu, J. / Du, L. / Liu, K. / Lu, L. / Zhang, R. / Jiang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cmu.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cmu.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 5cmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/5cmu ftp://data.pdbj.org/pub/pdb/validation_reports/cm/5cmu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8534.799 Da / Num. of mol.: 3 / Fragment: C-terminus (UNP RESIDUES 35-70) Source method: isolated from a genetically manipulated source Details: The fusion protein of expression tag, C-terminus residues 35-70 from gp4 and Artificial inhibitor AP1 Source: (gene. exp.) Human immunodeficiency virus 1, (gene. exp.) synthetic construct (others) Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q1HMR5, UniProt: P04578*PLUS #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 32% (w/v) PEG 3350, 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→31.03 Å / % possible obs: 99.1 % / Redundancy: 3.6 % / Net I/σ(I): 16.9 |
-Processing
Software |
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Refinement | Resolution: 2.113→31.03 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.9 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.113→31.03 Å
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Refine LS restraints |
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LS refinement shell |
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