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Yorodumi- PDB-4fz8: Crystal structure of C11 Fab, an ADCC mediating anti-HIV-1 antibody. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fz8 | ||||||
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Title | Crystal structure of C11 Fab, an ADCC mediating anti-HIV-1 antibody. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ADCC / ANTI-HIV-1 ENV ANTIBODY C11 / CD4I ANTIBODY / FAB / VIRAL GLYCOPROTEIN GP120 / HIV-1 ENV | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | ||||||
Authors | Wu, X. / Tolbert, W.D. / Pazgier, M. | ||||||
Citation | Journal: Mbio / Year: 2020 Title: Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial. Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. ...Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. / Lewis, G.K. / Pazgier, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fz8.cif.gz | 185.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fz8.ent.gz | 148.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/4fz8 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/4fz8 | HTTPS FTP |
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-Related structure data
Related structure data | 6mg7C 6oedC 6oejC 6ofiC 3tnnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25403.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23710.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo Sapiens (human) |
#3: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 294 K / pH: 7.5 Details: 0.14 M sodium citrate, 0.07 M HEPES sodium pH 7.5, 14% isopropanol, and 30% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2012 / Details: K-B FOCUSING MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→50 Å / Num. obs: 14023 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.3 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TNN Resolution: 2.66→34.35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 53.222 / SU ML: 0.467 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.66→34.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.732 Å / Total num. of bins used: 20
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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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