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- PDB-3se8: Crystal structure of broadly and potently neutralizing antibody V... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3se8 | ||||||
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Title | Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with HIV-1 gp120 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / HIV / GP120 / ANTIBODY / VRC03 / 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 / virion membrane / structural molecule activity / 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 468.8 KB | Display | ![]() |
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PDB format | ![]() | 403.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 508.3 KB | Display | ![]() |
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Full document | ![]() | 521.8 KB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25294.525 Da / Num. of mol.: 1 / Fragment: Antigen binding fragement of antibody heavy chain Source method: isolated from a genetically manipulated source Details: Co-transfection of both heavy and light chain plasmids Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 23146.795 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, 12 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 truncations Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 654 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 9 % PEG 4000, 200 mM Li2SO4, 100 mM Tris/Cl-, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.895→50 Å / Num. all: 76674 / Num. obs: 69237 / % possible obs: 90.3 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.82 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.895→37.032 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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