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- PDB-4jpv: Crystal structure of broadly and potently neutralizing antibody 3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jpv | ||||||
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Title | Crystal structure of broadly and potently neutralizing antibody 3bnc117 in complex with hiv-1 gp120 | ||||||
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![]() | viral protein/immune system / HIV / GP120 / CD4-BINDING SITE / 3BNC117 / NEUTRALIZATION / VACCINE / ANTIBODY / ENVELOPE PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | ![]() 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 ...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 / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, T. / Moquin, S. / Kwong, P.D. | ||||||
![]() | ![]() Title: Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization. Authors: Klein, F. / Diskin, R. / Scheid, J.F. / Gaebler, C. / Mouquet, H. / Georgiev, I.S. / Pancera, M. / Zhou, T. / Incesu, R.B. / Fu, B.Z. / Gnanapragasam, P.N. / Oliveira, T.Y. / Seaman, M.S. / ...Authors: Klein, F. / Diskin, R. / Scheid, J.F. / Gaebler, C. / Mouquet, H. / Georgiev, I.S. / Pancera, M. / Zhou, T. / Incesu, R.B. / Fu, B.Z. / Gnanapragasam, P.N. / Oliveira, T.Y. / Seaman, M.S. / Kwong, P.D. / Bjorkman, P.J. / Nussenzweig, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327.6 KB | Display | ![]() |
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PDB format | ![]() | 265.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.5 KB | Display | ![]() |
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Full document | ![]() | 517.1 KB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gw4C ![]() 4jpwC ![]() 3se9S 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
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24656.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 23022.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 12 molecules G![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 39182.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 86 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-EPE / | ||
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#6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 11% PEG 8000, 7% ethylene glycol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Dec 5, 2011 |
Radiation | Monochromator: APS 22-BM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 27456 / Num. obs: 27017 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.62 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SE9 Resolution: 2.827→48.966 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 28.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.806 Å2 / ksol: 0.353 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.827→48.966 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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