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- PDB-1yyl: crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in co... -
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Open data
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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 | |||||||||
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![]() | Viral protein/Immune system / HIV-1 / gp120 / YU2 / scorpion toxin / CD4 mimic / CD4M33 / antibody / Viral protein-Immune system COMPLEX | |||||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 | ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321.3 KB | Display | ![]() |
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PDB format | ![]() | 254.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 522.5 KB | Display | ![]() |
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Full document | ![]() | 577.1 KB | Display | |
Data in XML | ![]() | 64.7 KB | Display | |
Data in CIF | ![]() | 89 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yymC ![]() 1rzkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELLCLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: ![]() ![]() #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.) ![]() Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELLCLONE FUSED WITH A MURINE B-CELL FUSION PARTNER Production host: ![]() ![]() |
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-Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 344 molecules GPMS![](data/chem/img/NAG.gif)
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#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.) ![]() ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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