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Yorodumi- PDB-4dko: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -
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-Basic information
Entry | Database: PDB / ID: 4dko | ||||||
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Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with TS-II-224 | ||||||
Components | HIV-1 gp120 core | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / HIV-1 gp120 / clade A/E / CD4 mimic / TS-II-224 / VIRAL PROTEIN-INHIBITOR 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å | ||||||
Authors | Kwon, Y.D. / LaLonde, J.M. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Mascola, J. ...Kwon, Y.D. / LaLonde, J.M. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Mascola, J. / Schon, A. / Freire, E. / Sodroski, J. / Madani, N. / Smith III, A.B. / Kwong, P.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors. Authors: Lalonde, J.M. / Kwon, Y.D. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Schon, A. / Freire, E. / Kwong, P.D. / Mascola, J.R. / ...Authors: Lalonde, J.M. / Kwon, Y.D. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Schon, A. / Freire, E. / Kwong, P.D. / Mascola, J.R. / Sodroski, J. / Madani, N. / Smith, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dko.cif.gz | 299.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dko.ent.gz | 243.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/4dko ftp://data.pdbj.org/pub/pdb/validation_reports/dk/4dko | HTTPS FTP |
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-Related structure data
Related structure data | 4dkpC 4dkqC 4dkrC 3tgtS C: citing same article (ref.) 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 | Mass: 39160.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: clade A/E 93TH057 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS #2: Sugar | ChemComp-NAG / #3: Chemical | #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: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 8000, 5% iso-propanol, 0.1M HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.981→50 Å / Num. all: 57477 / Num. obs: 54086 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.099 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.54 / Num. unique all: 2120 / Rsym value: 0.493 / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TGT Resolution: 1.981→41.941 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.655 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.63 Å2 / Biso mean: 43.1748 Å2 / Biso min: 11.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.981→41.941 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: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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