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Yorodumi- PDB-1yym: crystal structure of F23, a scorpion-toxin mimic of CD4, in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yym | |||||||||
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Title | crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b | |||||||||
Components |
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Keywords | Viral protein/Immune system / HIV-1 / gp120 / YU2 / scorpion toxin / CD4 mimic / F23 / antibody / Viral protein-Immune system COMPLEX | |||||||||
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 | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | |||||||||
Authors | Huang, C.C. / Stricher, F. / Martin, L. / Decker, J.M. / Majeed, S. / Barthe, P. / Hendrickson, W.A. / Robinson, J. / Roumestand, C. / Sodroski, J. ...Huang, C.C. / Stricher, F. / Martin, L. / Decker, J.M. / Majeed, S. / Barthe, P. / Hendrickson, W.A. / Robinson, J. / Roumestand, C. / Sodroski, J. / Wyatt, R. / Shaw, G.M. / Vita, C. / Kwong, P.D. | |||||||||
Citation | Journal: Structure / Year: 2005 Title: Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth. Authors: Huang, C.C. / Stricher, F. / Martin, L. / Decker, J.M. / Majeed, S. / Barthe, P. / Hendrickson, W.A. / Robinson, J. / Roumestand, C. / Sodroski, J. / Wyatt, R. / Shaw, G.M. / Vita, C. / Kwong, P.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yym.cif.gz | 333 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yym.ent.gz | 263.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/1yym ftp://data.pdbj.org/pub/pdb/validation_reports/yy/1yym | HTTPS FTP |
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-Related structure data
Related structure data | 1yylSC 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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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules LQHR
#2: Antibody | Mass: 23399.898 Da / Num. of mol.: 2 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELLCLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Mus musculus (house mouse) #3: Antibody | Mass: 24457.387 Da / Num. of mol.: 2 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELLCLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: Mus musculus (house mouse) |
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-Protein / Protein/peptide / Sugars , 3 types, 20 molecules GPMS
#1: Protein | Mass: 34838.691 Da / Num. of mol.: 2 Fragment: UNP residues 82-126,UNP residues 191-293,UNP residues 325-479 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P35961 #4: Protein/peptide | Mass: 2863.540 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: SYNTHETIC MINIPROTEIN (SOLID PHASE METHOD USING FMOC-PROTECTED AMINO ACIDS) Source: (synth.) synthetic construct (others) #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 793 molecules
#6: Chemical | #7: Chemical | #8: 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: 2.562 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, isopropanol, sodium citrate, pH 5.6, 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: MARRESEARCH / Detector: CCD / Date: Oct 31, 2003 |
Radiation | Monochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.34 / % possible all: 69.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1YYL Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 265543.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.3791 Å2 / ksol: 0.344526 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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