[English] 日本語
![](img/lk-miru.gif)
- PDB-3se9: Crystal structure of broadly and potently neutralizing antibody V... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3se9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with HIV-1 gp120 | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN/IMMUNE SYSTEM / HIV / GP120 / ANTIBODY / VRC-PG04 / NEUTRALIZATION / VACCINE / ENVELOPE GLYCOPROTEIN / 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 | ![]() ![]() ![]() | ||||||
![]() | Kwong, P.D. / Zhou, T. | ||||||
![]() | ![]() Title: Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. ...Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. / Yang, Z.Y. / Yang, Z. / Zhang, Z. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Simek, M. / Burton, D.R. / Koff, W.C. / Doria-Rose, N.A. / Connors, M. / Mullikin, J.C. / Nabel, G.J. / Roederer, M. / Shapiro, L. / Kwong, P.D. / Mascola, J.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 458.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 395.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 532.7 KB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24644.771 Da / Num. of mol.: 1 / Fragment: Antigen binding fragement of heavy chain Source method: isolated from a genetically manipulated source Details: Co-transfection of both heavy and light chain plasmids Source: (gene. exp.) ![]() ![]() |
---|---|
#3: Antibody | Mass: 23073.822 Da / Num. of mol.: 1 / Fragment: antibody light chain Source method: isolated from a genetically manipulated source Details: Co-transfection of both heavy and light chain plasmids Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 11 molecules G![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: Core gp120 with trancations Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 584 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BU3.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BU3.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-BU3 / ( | #9: Chemical | ChemComp-TRS / | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 9.9% PEG 4000, 9.0 % isopropanol, 100 mM Li2SO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 67230 / Num. obs: 59364 / % possible obs: 88.3 % |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.269 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→23.734 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|