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Yorodumi- PDB-8gd5: Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gd5 | ||||||
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Title | Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Complex with DL-I-102 | ||||||
Components | HIV-1 LM/HS clade A/E CRF01 gp120 core | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / HIV-1 GP120 / CLADE A/E CF01 / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Chem-Z2O / 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: 2.6 Å | ||||||
Authors | Tolbert, W.D. / Nguyen, D.N. / Pazgier, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Viruses / Year: 2023 Title: Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC. Authors: Ding, S. / Tolbert, W.D. / Zhu, H. / Lee, D. / Marchitto, L. / Higgins, T. / Zhao, X. / Nguyen, D. / Sherburn, R. / Richard, J. / Gendron-Lepage, G. / Medjahed, H. / Mohammadi, M. / Abrams, ...Authors: Ding, S. / Tolbert, W.D. / Zhu, H. / Lee, D. / Marchitto, L. / Higgins, T. / Zhao, X. / Nguyen, D. / Sherburn, R. / Richard, J. / Gendron-Lepage, G. / Medjahed, H. / Mohammadi, M. / Abrams, C. / Pazgier, M. / Smith III, 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 | 8gd5.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gd5.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 8gd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gd5_validation.pdf.gz | 720.9 KB | Display | wwPDB validaton report |
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Full document | 8gd5_full_validation.pdf.gz | 731.7 KB | Display | |
Data in XML | 8gd5_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 8gd5_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/8gd5 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/8gd5 | HTTPS FTP |
-Related structure data
Related structure data | 8gczC 8gd0C 8gd1C 8gd3C 8gjtC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39452.723 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 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9 | ||||||||
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#2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-EPE / | #4: Chemical | ChemComp-Z2O / { | #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: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 3350 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 EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2022 |
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: 2.6→50 Å / Num. obs: 10748 / % possible obs: 86.1 % / Redundancy: 3.7 % / CC1/2: 0.94 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.09 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 562 / CC1/2: 0.6 / Rpim(I) all: 0.65 / % possible all: 90.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→32.54 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.53 / 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: 2.6→32.54 Å
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Refine LS restraints |
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LS refinement shell |
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