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- PDB-5drz: Crystal structure of anti-HIV-1 antibody F240 Fab in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5drz | ||||||
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Title | Crystal structure of anti-HIV-1 antibody F240 Fab in complex with gp41 peptide | ||||||
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![]() | IMMUNE SYSTEM / IgG / VIRAL PROTEIN / HIV gp41 ENVELOPE PROTEIN | ||||||
Function / homology | ![]() virus-mediated perturbation of host defense response => GO:0019049 / : / virion component => GO:0044423 / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / 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 ...virus-mediated perturbation of host defense response => GO:0019049 / : / virion component => GO:0044423 / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / 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 / membrane => GO:0016020 / 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 / structural molecule activity / virion membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gohain, N. / Tolbert, W.D. / Pazgier, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240. Authors: Gohain, N. / Tolbert, W.D. / Orlandi, C. / Richard, J. / Ding, S. / Chen, X. / Bonsor, D.A. / Sundberg, E.J. / Lu, W. / Ray, K. / Finzi, A. / Lewis, G.K. / Pazgier, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 362.4 KB | Display | ![]() |
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PDB format | ![]() | 296 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.4 KB | Display | ![]() |
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Full document | ![]() | 478.3 KB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 47.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tnnS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Antibody | Mass: 24363.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24970.748 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein/peptide | Mass: 4085.668 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG 3350, 15% Isopropanol, 0.2M Ammonium citrate pH4.5 PH range: 4.0-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2013 / Details: RH coated flat mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9753 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→168.79 Å / Num. all: 33289 / Num. obs: 33289 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.54→2.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 1.4 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TNN Resolution: 2.54→168.79 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 29.977 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.996 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.223 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→168.79 Å
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