[English] 日本語
Yorodumi- PDB-6vbq: Crystal structure of anti-HIV-1 antibody DH822 bound to gp120 V2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vbq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-HIV-1 antibody DH822 bound to gp120 V2 peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/Viral Protein / Antibody / GP120 V2 / RV305/RV144 / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex | ||||||
Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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 | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.116 Å | ||||||
Authors | Janus, B.M. / Ofek, G. | ||||||
Citation | Journal: JCI Insight / Year: 2020 Title: HIV vaccine delayed boosting increases Env variable region 2-specific antibody effector functions. Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Janus, B. / Gohain, N. / Williams, L.D. / Tay, M.Z. / Monroe, A. / Peachman, K. / Choe, M. / Min, S. / Lusso, P. / Zhang, P. / Go, E.P. / Desaire, H. ...Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Janus, B. / Gohain, N. / Williams, L.D. / Tay, M.Z. / Monroe, A. / Peachman, K. / Choe, M. / Min, S. / Lusso, P. / Zhang, P. / Go, E.P. / Desaire, H. / Bonsignori, M. / Hwang, K.K. / Beck, C. / Kakalis, M. / O'Connell, R.J. / Vasan, S. / Kim, J.H. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. / Kaewkungwal, J. / Pitisuttithum, P. / Nitayaphan, S. / Sinangil, F. / Tartaglia, J. / Phogat, S. / Wiehe, K. / Saunders, K.O. / Montefiori, D.C. / Tomaras, G.D. / Moody, M.A. / Arthos, J. / Rao, M. / Joyce, M.G. / Ofek, G.A. / Ferrari, G. / Haynes, B.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vbq.cif.gz | 641.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vbq.ent.gz | 536.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/6vbq ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vbq | HTTPS FTP |
---|
-Related structure data
Related structure data | 6vboC 6vbpC 4hk0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24669.748 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23004.482 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein/peptide | Mass: 2675.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: I2E6B7 #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.33 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 18% 2-propanol, 20% PEG 4000, 0.1M sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.116→50 Å / Num. obs: 112193 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rpim(I) all: 0.053 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.116→2.15 Å / Num. unique obs: 7725 / Rpim(I) all: 0.304 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HK0 Resolution: 2.116→40.678 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.71 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.73 Å2 / Biso mean: 50.1984 Å2 / Biso min: 16.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.116→40.678 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|