[English] 日本語
Yorodumi- PDB-8gd3: Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gd3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Complex with DL-I-101 | ||||||
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 / DI(HYDROXYETHYL)ETHER / Chem-Z1Z / 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: 2.19 Å | ||||||
Authors | Tolbert, W.D. / Nguyen, D.N. / Pazgier, M. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gd3.cif.gz | 85 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gd3.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 8gd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/8gd3 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/8gd3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8gczC 8gd0C 8gd1C 8gd5C 8gjtC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 11 molecules A
#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 |
---|---|
#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 67 molecules
#3: Chemical | ChemComp-EPE / |
---|---|
#4: Chemical | ChemComp-Z1Z / ( |
#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 3350 10% PEG 400 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 2.19→50 Å / Num. obs: 20214 / % possible obs: 97.4 % / Redundancy: 4.3 % / CC1/2: 1 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.097 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.19→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 865 / CC1/2: 0.65 / Rpim(I) all: 0.364 / % possible all: 85 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→28.4 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.11 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→28.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|