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Yorodumi- PDB-1yyl: crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yyl | |||||||||
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Title | crystal structure of CD4M33, 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 / CD4M33 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.75 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 | 1yyl.cif.gz | 321.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yyl.ent.gz | 254.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/1yyl ftp://data.pdbj.org/pub/pdb/validation_reports/yy/1yyl | HTTPS FTP |
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-Related structure data
Related structure data | 1yymC 1rzkS 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
-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 / Non-polymers , 4 types, 344 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: 2939.635 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 / #6: 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: 2.593 Å3/Da / Density % sol: 52.6 % |
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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: Jun 5, 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: 2.75→20 Å / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.278 / % possible all: 46.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RZK Resolution: 2.75→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 193480.34 / 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: 27.8683 Å2 / ksol: 0.340928 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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