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- PDB-8e1p: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e1p | ||||||
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Title | Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / HIV envelope glycoprotein / antibody / CD4 antibody / VIRAL PROTEIN-IMMUNE SYSTEM / 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 / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sarkar, A. / Kumar, S. / Wilson, I.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions. Authors: Caniels, T.G. / Medina-Ramirez, M. / Zhang, J. / Sarkar, A. / Kumar, S. / LaBranche, A. / Derking, R. / Allen, J.D. / Snitselaar, J.L. / Capella-Pujol, J. / Sanchez, I.D.M. / Yasmeen, A. / ...Authors: Caniels, T.G. / Medina-Ramirez, M. / Zhang, J. / Sarkar, A. / Kumar, S. / LaBranche, A. / Derking, R. / Allen, J.D. / Snitselaar, J.L. / Capella-Pujol, J. / Sanchez, I.D.M. / Yasmeen, A. / Diaz, M. / Aldon, Y. / Bijl, T.P.L. / Venkatayogi, S. / Martin Beem, J.S. / Newman, A. / Jiang, C. / Lee, W.H. / Pater, M. / Burger, J.A. / van Breemen, M.J. / de Taeye, S.W. / Rantalainen, K. / LaBranche, C. / Saunders, K.O. / Montefiori, D. / Ozorowski, G. / Ward, A.B. / Crispin, M. / Moore, J.P. / Klasse, P.J. / Haynes, B.F. / Wilson, I.A. / Wiehe, K. / Verkoczy, L. / Sanders, R.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 989 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9 MB | Display | ![]() |
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Full document | ![]() | 9.2 MB | Display | |
Data in XML | ![]() | 150.1 KB | Display | |
Data in CIF | ![]() | 200.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w6dS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 6 molecules EGMYXZ
#5: Protein | Mass: 53394.711 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #7: Protein | Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Antibody , 5 types, 12 molecules FHNILOACJBDK
#1: Antibody | Mass: 24399.408 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | | Mass: 22229.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 22229.459 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 23056.605 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Antibody | Mass: 25460.508 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 7 types, 47 molecules ![](data/chem/img/NAG.gif)
#8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #9: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #11: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 1600.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #12: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #13: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source #14: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.63 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 12% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→49.76 Å / Num. obs: 63948 / % possible obs: 95.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 104.91 Å2 / CC1/2: 0.78 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3.82→3.88 Å / Num. unique obs: 5699 / CC1/2: 0.31 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5W6D Resolution: 3.82→49.76 Å / SU ML: 0.6141 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 31.5444 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 122.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.82→49.76 Å
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Refine LS restraints |
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LS refinement shell |
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