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Yorodumi- PDB-3egs: Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3egs | ||||||
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Title | Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671 soaked in ammonium sulfate | ||||||
Components |
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Keywords | IMMUNE SYSTEM / 2F5 / gp41 / HIV | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Julien, J.-P. / Bryson, S. / de la Torre, B.G. / Andreu, D. / Nieva, J.L. / Pai, E.F. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2009 Title: Structural constraints imposed by the conserved fusion peptide on the HIV-1 gp41 epitope recognized by the broadly neutralizing antibody 2F5. Authors: de la Arada, I. / Julien, J.P. / de la Torre, B.G. / Huarte, N. / Andreu, D. / Pai, E.F. / Arrondo, J.L. / Nieva, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3egs.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3egs.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 3egs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3egs_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 3egs_full_validation.pdf.gz | 455.8 KB | Display | |
Data in XML | 3egs_validation.xml.gz | 18 KB | Display | |
Data in CIF | 3egs_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/3egs ftp://data.pdbj.org/pub/pdb/validation_reports/eg/3egs | HTTPS FTP |
-Related structure data
Related structure data | 3drtC 3d0lS 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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Unit cell |
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-Components
#1: Antibody | Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 24985.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#3: Protein/peptide | Mass: 3822.411 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized by Fmoc chemistry. The sequence of the peptide is naturally found in the human immunodeficiency virus. |
Nonpolymer details | ACA IN THE PEPTIDE SEQUENCE STANDS FOR 6-AMINO-HEXANOIC ACID LINKER. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Growth: 0.1 M sodium acetate, pH 5.6, 16-20% 2-propanol, 16-20% PEG 4K. Soak: 0.1 M sodium acetate, pH 5.6, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2008 / Details: Micromax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→17 Å / Num. all: 5537 / Num. obs: 5386 / % possible obs: 95.5 % / Redundancy: 3.8 % / Rsym value: 0.28 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 3.6→3.7 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3 / Num. unique all: 418 / Rsym value: 0.462 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D0L Resolution: 3.6→16.73 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1744119.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 1.55999 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.6→16.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.82 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Xplor file |
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