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Yorodumi- PDB-6onh: Crystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6onh | ||||||||||||
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Title | Crystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in complex with (S)-MCG-IV-031-A05. | ||||||||||||
Components | HIV-1 LM/HT Clade A/E CRF01 gp120 | ||||||||||||
Keywords | viral protein/inhibitor / HIV-1 gp120 / CLADE A/E CF01 / viral protein / viral protein-inhibitor complex | ||||||||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Chem-MWD / clade A/E 93TH057 HIV-1 gp120 core Function and homology information | ||||||||||||
Biological species | Human immunodeficiency virus 1 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å | ||||||||||||
Authors | Tolbert, W.D. / Sherburn, R. / Pazgier, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Virol. / Year: 2019 Title: A New Family of Small-Molecule CD4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of HIV-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity. Authors: Ding, S. / Grenier, M.C. / Tolbert, W.D. / Vezina, D. / Sherburn, R. / Richard, J. / Prevost, J. / Chapleau, J.P. / Gendron-Lepage, G. / Medjahed, H. / Abrams, C. / Sodroski, J. / Pazgier, M. ...Authors: Ding, S. / Grenier, M.C. / Tolbert, W.D. / Vezina, D. / Sherburn, R. / Richard, J. / Prevost, J. / Chapleau, J.P. / Gendron-Lepage, G. / Medjahed, H. / Abrams, C. / Sodroski, J. / Pazgier, M. / Smith 3rd, A.B. / Finzi, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6onh.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6onh.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 6onh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6onh_validation.pdf.gz | 714.4 KB | Display | wwPDB validaton report |
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Full document | 6onh_full_validation.pdf.gz | 721.5 KB | Display | |
Data in XML | 6onh_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6onh_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/6onh ftp://data.pdbj.org/pub/pdb/validation_reports/on/6onh | HTTPS FTP |
-Related structure data
Related structure data | 6oneC 6onfC 6onvC 6p9nC 3tgtS 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 | Mass: 39466.750 Da / Num. of mol.: 1 / Mutation: H61Y, Q105H, V108I, H375T, N474D, I475M, K476R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9 | ||||||||
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#2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-MWD / ( | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 1500 5% PEG 400 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 15219 / % possible obs: 80.6 % / Redundancy: 3.1 % / CC1/2: 0.96 / Rpim(I) all: 0.107 / Rsym value: 0.165 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.24→2.37 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 2436 / CC1/2: 0.45 / Rpim(I) all: 0.364 / Rsym value: 0.557 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TGT Resolution: 2.244→52.74 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.43 / 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: 2.244→52.74 Å
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Refine LS restraints |
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LS refinement shell |
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