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Yorodumi- PDB-3aha: Crystal structure of the complex between gp41 fragments N36 and C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aha | ||||||
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Title | Crystal structure of the complex between gp41 fragments N36 and C34 mutant N126K/E137Q | ||||||
Components | (Transmembrane protein gp41Transmembrane protein) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / coiled-coil / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Dectin-2 family / 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 ...Dectin-2 family / 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 / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Izumi, K. / Nakamura, S. / Nakano, H. / Shimura, K. / Sakagami, Y. / Oishi, S. / Uchiyama, S. / Ohkubo, T. / Kobayashi, Y. / Fujii, N. ...Izumi, K. / Nakamura, S. / Nakano, H. / Shimura, K. / Sakagami, Y. / Oishi, S. / Uchiyama, S. / Ohkubo, T. / Kobayashi, Y. / Fujii, N. / Matsuoka, M. / Kodama, E.N. | ||||||
Citation | Journal: Antiviral Res. / Year: 2010 Title: Characterization of HIV-1 resistance to a fusion inhibitor, N36, derived from the gp41 amino terminal heptad repeat. Authors: Izumi, K. / Nakamura, S. / Nakano, H. / Shimura, K. / Sakagami, Y. / Oishi, S. / Uchiyama, S. / Ohkubo, T. / Kobayashi, Y. / Fujii, N. / Matsuoka, M. / Kodama, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aha.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aha.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 3aha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3aha ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3aha | HTTPS FTP |
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-Related structure data
Related structure data | 1aikS 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4208.886 Da / Num. of mol.: 3 / Fragment: gp41 fragment N36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q72502, UniProt: Q70626*PLUS #2: Protein/peptide | Mass: 4289.715 Da / Num. of mol.: 3 / Fragment: gp41 fragment C34 / Mutation: N126K, E137Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q70626 #3: Chemical | ChemComp-MPD / ( | #4: Chemical | #5: 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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 80mM ammonium chloride, 16% 2-methylpentan-2,4-diol, 25% isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35 Å / Num. obs: 27434 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Redundancy: 3.61 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 1.7→1.74 Å / % possible all: 99.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AIK Resolution: 1.7→23.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.874 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.491 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→23.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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