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- PDB-3drt: Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3drt | ||||||
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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 | ||||||
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![]() | IMMUNE SYSTEM / HIV-1 / gp41 / 2F5 / nmAb | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Julien, J.-P. / Bryson, S. / de la Torre, B.G. / Andreu, D. / Nieva, J.L. / Pai, E.F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.6 KB | Display | ![]() |
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PDB format | ![]() | 71.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461 KB | Display | ![]() |
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Full document | ![]() | 475.5 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3egsC ![]() 3d0lS ![]() 3drv S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Antibody | Mass: 24985.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#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. |
#4: Chemical | ChemComp-GOL / |
Nonpolymer details | ACA IN THE PEPTIDE SEQUENCE STANDS FOR 6-AMINO-HEXANOIC ACID LINKER. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Crystals were grown in reservoir solution containing 0.1 M Na citrate pH 5.6, 16% 2-propanol, 16% PEG 4K, 0.01% Tween-20, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→17 Å / Num. all: 7263 / Num. obs: 6826 / % possible obs: 94 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.265 |
Reflection shell | Resolution: 3.3→3.51 Å / Redundancy: 8.15 % / Rmerge(I) obs: 0.497 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3D0L Resolution: 3.3→16.81 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 508628.56 / 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: 10.7845 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→16.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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