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Yorodumi- PDB-5if0: Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5if0 | ||||||
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Title | Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.44 A | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 gp120 / engineered outer domain (eOD) / germline targeting / CD4 binding site / VRC01-class naive human germline antibody / immune system / viral-protein complex / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Sarkar, A. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 2016 Title: HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen. Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / ...Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / Georgeson, E. / Adachi, Y. / Kubitz, M. / deCamp, A.C. / Julien, J.P. / Wilson, I.A. / Burton, D.R. / Crotty, S. / Schief, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5if0.cif.gz | 466.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5if0.ent.gz | 384.6 KB | Display | PDB format |
PDBx/mmJSON format | 5if0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/5if0 ftp://data.pdbj.org/pub/pdb/validation_reports/if/5if0 | HTTPS FTP |
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-Related structure data
Related structure data | 5idlC 5iesC 5ifaC 4jpkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules AHBL
#1: Antibody | Mass: 23614.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSEss-CHIg-hG1 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human) #2: Antibody | Mass: 23816.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSEss-CHIg-hG1 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human) |
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-Protein / Sugars , 2 types, 6 molecules GI
#3: Protein | Mass: 19889.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 77 molecules
#5: Chemical | ChemComp-PO4 / |
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#6: 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: 3.97 Å3/Da / Density % sol: 69.04 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium dihydrogen phosphate, 20% (w/v) PEG3350 and cryo-protected with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.408→44.444 Å / Num. obs: 73979 / % possible obs: 95.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 47.6 Å2 / CC1/2: 0.849 / Rsym value: 0.0102 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.4082→2.4399 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.1 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JPK Resolution: 2.44→44.444 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.84 / 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: 2.44→44.444 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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