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- PDB-4ye4: Crystal Structure of Neutralizing Antibody HJ16 in Complex with H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ye4 | ||||||
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Title | Crystal Structure of Neutralizing Antibody HJ16 in Complex with HIV-1 gp120 | ||||||
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![]() | Viral protein/Immune system / HIV1 / antibody / gp120 / complex / Viral protein-Immune system complex | ||||||
Function / homology | ![]() virus-mediated perturbation of host defense response => GO:0019049 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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. / Chen, L. / Zhou, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Authors: Zhou, T. / Lynch, R.M. / Chen, L. / Acharya, P. / Wu, X. / Doria-Rose, N.A. / Joyce, M.G. / Lingwood, D. / Soto, C. / Bailer, R.T. / Ernandes, M.J. / Kong, R. / Longo, N.S. / Louder, M.K. / ...Authors: Zhou, T. / Lynch, R.M. / Chen, L. / Acharya, P. / Wu, X. / Doria-Rose, N.A. / Joyce, M.G. / Lingwood, D. / Soto, C. / Bailer, R.T. / Ernandes, M.J. / Kong, R. / Longo, N.S. / Louder, M.K. / McKee, K. / O'Dell, S. / Schmidt, S.D. / Tran, L. / Yang, Z. / Druz, A. / Luongo, T.S. / Moquin, S. / Srivatsan, S. / Yang, Y. / Zhang, B. / Zheng, A. / Pancera, M. / Kirys, T. / Georgiev, I.S. / Gindin, T. / Peng, H.P. / Yang, A.S. / Mullikin, J.C. / Gray, M.D. / Stamatatos, L. / Burton, D.R. / Koff, W.C. / Cohen, M.S. / Haynes, B.F. / Casazza, J.P. / Connors, M. / Corti, D. / Lanzavecchia, A. / Sattentau, Q.J. / Weiss, R.A. / West Jr., A.P. / Bjorkman, P.J. / Scheid, J.F. / Nussenzweig, M.C. / Shapiro, L. / Mascola, J.R. / Kwong, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.7 KB | Display | ![]() |
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PDB format | ![]() | 265.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 482.6 KB | Display | |
Data in XML | ![]() | 29.6 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rwyC ![]() 4rx4C ![]() 4ydiC ![]() 4ydjC ![]() 4ydkC ![]() 4ydlC ![]() 4yflC C: citing same article ( |
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Similar 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
#1: Protein | Mass: 39492.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HIV-1 clade B gp120 core / Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Antibody | Mass: 24606.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Antibody | Mass: 24202.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M imidazole pH 6.5 10 % (W/V) PEG 8000 5% isopropanol PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2013 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→41.9 Å / Num. obs: 20510 / % possible obs: 94.4 % / Redundancy: 4.6 % / Net I/σ(I): 1.98 |
Reflection shell | Highest resolution: 2.72 Å |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.81 Å2 / Biso mean: 60.9245 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.72→41.9 Å
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LS refinement shell | Highest resolution: 2.72 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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