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Yorodumi- PDB-3f50: HIV gp41 six-helix bundle composed of an alpha/beta-peptide analo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f50 | |||||||||
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Title | HIV gp41 six-helix bundle composed of an alpha/beta-peptide analogue of the CHR domain in complex with an NHR domain alpha-peptide | |||||||||
Components |
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Keywords | VIRAL PROTEIN / alpha/beta-peptide / helix bundle / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Envelope protein / Fusion protein / Glycoprotein / Host-virus interaction / Lipoprotein / Membrane / Palmitate / Transmembrane / Viral immunoevasion / Virion | |||||||||
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 Similarity search - Function | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Horne, W.S. / Gellman, S.H. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural and biological mimicry of protein surface recognition by alpha/beta-peptide foldamers Authors: Horne, W.S. / Johnson, L.M. / Ketas, T.J. / Klasse, P.J. / Lu, M. / Moore, J.P. / Gellman, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f50.cif.gz | 28 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f50.ent.gz | 17.4 KB | Display | PDB format |
PDBx/mmJSON format | 3f50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f50 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f50 | HTTPS FTP |
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-Related structure data
Related structure data | 3f4ySC 3f4zSC 3g7aC S: Starting model for refinement C: citing same article (ref.) |
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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.: 1 / Fragment: UNP RESIDUES 545 TO 580 / Source method: obtained synthetically Details: The peptide is chemically synthesized. It is found naturally in HIV. References: UniProt: P04580 |
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#2: Protein/peptide | Mass: 4526.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide. |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M NaCl, 0.1 M Tris pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2008 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 2893 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rsym value: 0.061 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.512 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 3F4Y and 3F4Z Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.884 / SU B: 18.055 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.71 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 74.307 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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