+Open data
-Basic information
Entry | Database: PDB / ID: 6xlz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of NHP D11A.F2 Fab in complex with 16055 V2b peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Fab / HIV / V1V2 / Complex / Antibody / Scaffold / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information 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 / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Aljedani, S. / Rodarte, J. / Liban, T. / Pancera, M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Plos Pathog. / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xlz.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xlz.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/6xlz ftp://data.pdbj.org/pub/pdb/validation_reports/xl/6xlz | HTTPS FTP |
---|
-Related structure data
Related structure data | 6vjnC 6wasC 6witC 6xsnC 4rfoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-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.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: A0A0B5KUY7 |
---|
-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.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
---|---|
#3: Antibody | Mass: 23359.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 111 molecules
#4: Chemical | ChemComp-BU3 / ( #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.17 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|