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Open data
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Basic information
Entry | Database: PDB / ID: 6xlz | ||||||
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Title | Structure of NHP D11A.F2 Fab in complex with 16055 V2b peptide | ||||||
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![]() | IMMUNE SYSTEM / Fab / HIV / V1V2 / Complex / Antibody / Scaffold / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() virus-mediated perturbation of host defense response => GO:0019049 / : / 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 ...virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aljedani, S. / Rodarte, J. / Liban, T. / Pancera, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization. Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / ...Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / O'Dell, S. / Mascola, J.R. / Lee, K.K. / Karlsson Hedestam, G.B. / Wyatt, R.T. / Pancera, 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 | ![]() | 185.1 KB | Display | ![]() |
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PDB format | ![]() | 146.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477 KB | Display | ![]() |
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Full document | ![]() | 477.4 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vjnC ![]() 6wasC ![]() 6witC ![]() 6xsnC ![]() 4rfoS 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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1 |
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Unit cell |
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Components
-Protein/peptide , 1 types, 2 molecules PA
#1: Protein/peptide | Mass: 2738.150 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 23688.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Antibody | Mass: 23359.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 111 molecules ![](data/chem/img/BU3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BU3 / ( #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris pH 8.0 and 1.32 M K/Na Tartrate at 8.5 mg/ml. Cryo protection: 15% 2R3R Butanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→94.22 Å / Num. obs: 21787 / % possible obs: 99.8 % / Redundancy: 22.2 % / Biso Wilson estimate: 52.57 Å2 / CC1/2: 0.72 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 22.2 % / Num. unique obs: 3087 / CC1/2: 0.744 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RFO Resolution: 2.8→94.21 Å / SU ML: 0.2148 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6378 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→94.21 Å
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Refine LS restraints |
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LS refinement shell |
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