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Yorodumi- PDB-6ol7: Crystal structure of glVRC01 scFv in complex with anti-idiotype i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ol7 | ||||||||||||
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Title | Crystal structure of glVRC01 scFv in complex with anti-idiotype iv8 scFv | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / glVRC01 / Iv8 / Anti-Idiotype / scFv / antibody / HIV | ||||||||||||
Function / homology | DI(HYDROXYETHYL)ETHER Function and homology information | ||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.419 Å | ||||||||||||
Authors | Weidle, C. / Pancera, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Exp.Med. / Year: 2019 Title: Anti-idiotypic antibodies elicit anti-HIV-1-specific B cell responses. Authors: Dosenovic, P. / Pettersson, A.K. / Wall, A. / Thientosapol, E.S. / Feng, J. / Weidle, C. / Bhullar, K. / Kara, E.E. / Hartweger, H. / Pai, J.A. / Gray, M.D. / Parks, K.R. / Taylor, J.J. / ...Authors: Dosenovic, P. / Pettersson, A.K. / Wall, A. / Thientosapol, E.S. / Feng, J. / Weidle, C. / Bhullar, K. / Kara, E.E. / Hartweger, H. / Pai, J.A. / Gray, M.D. / Parks, K.R. / Taylor, J.J. / Pancera, M. / Stamatatos, L. / Nussenzweig, M.C. / McGuire, A.T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ol7.cif.gz | 699.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ol7.ent.gz | 583.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ol7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/6ol7 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/6ol7 | HTTPS FTP |
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-Related structure data
Related structure data | 6mftS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Antibody , 4 types, 16 molecules AEKPBFLNCHIMDJOQ
#1: Antibody | Mass: 14527.015 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 11673.807 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 15607.272 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #4: Antibody | Mass: 13330.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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-Non-polymers , 4 types, 1187 molecules
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.68 % / Description: plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.13M NaCl, 0.13M Tris pH 8.0, 10.4% PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.419→50 Å / Num. obs: 87182 / % possible obs: 92.39 % / Redundancy: 1.7 % / Net I/σ(I): 10.25 |
Reflection shell | Resolution: 2.419→2.506 Å / Num. unique obs: 5909 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MFT Resolution: 2.419→49.784 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.419→49.784 Å
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Refine LS restraints |
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LS refinement shell |
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