[English] 日本語
Yorodumi- PDB-4jb9: Crystal structure of antibody VRC06 in complex with HIV-1 gp120 core -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jb9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of antibody VRC06 in complex with HIV-1 gp120 core | ||||||
Components |
| ||||||
Keywords | viral protein/immune system / HIV-1 / gp120 / antibody / VRC06 / glycoprotein / IMMUNE SYSTEM / viral protein-immune system 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 | HUMAN IMMUNODEFICIENCY VIRUS 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Kwon, Y.D. / Zhou, T. / Srivatsan, S. / Kwong, P.D. | ||||||
Citation | Journal: Science / Year: 2013 Title: Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization. Authors: Georgiev, I.S. / Doria-Rose, N.A. / Zhou, T. / Kwon, Y.D. / Staupe, R.P. / Moquin, S. / Chuang, G.Y. / Louder, M.K. / Schmidt, S.D. / Altae-Tran, H.R. / Bailer, R.T. / McKee, K. / Nason, M. ...Authors: Georgiev, I.S. / Doria-Rose, N.A. / Zhou, T. / Kwon, Y.D. / Staupe, R.P. / Moquin, S. / Chuang, G.Y. / Louder, M.K. / Schmidt, S.D. / Altae-Tran, H.R. / Bailer, R.T. / McKee, K. / Nason, M. / O'Dell, S. / Ofek, G. / Pancera, M. / Srivatsan, S. / Shapiro, L. / Connors, M. / Migueles, S.A. / Morris, L. / Nishimura, Y. / Martin, M.A. / Mascola, J.R. / Kwong, P.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jb9.cif.gz | 332.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jb9.ent.gz | 273.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/4jb9 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/4jb9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4j6rC 3se8S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39211.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo Sapiens (human) / References: UniProt: Q0ED31*PLUS | ||
---|---|---|---|
#2: Antibody | Mass: 25362.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: homo sapiens (human) | ||
#3: Antibody | Mass: 23014.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human) | ||
#4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% PEG 4000, 0.2M sodium acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 31045 / Num. obs: 29132 / % possible obs: 92.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.1 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.375 / Num. unique all: 909 / Rsym value: 0.412 / % possible all: 57.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: 3SE8 Resolution: 2.6→48.72 Å / SU ML: 0.41 / σ(F): 1.36 / Phase error: 36.98 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.72 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|