+Open data
-Basic information
Entry | Database: PDB / ID: 4jha | ||||||
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Title | Crystal Structure of RSV-Neutralizing Human Antibody D25 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin / Ig | ||||||
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: 1.6 Å | ||||||
Authors | Mclellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. ...Mclellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / Kwong, P.D. / Graham, B.S. | ||||||
Citation | Journal: Science / Year: 2013 Title: Structure of RSV fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody. Authors: McLellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / ...Authors: McLellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / Kwong, P.D. / Graham, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jha.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jha.ent.gz | 149.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jha ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jha | HTTPS FTP |
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-Related structure data
Related structure data | 4jhwC 3gbmS 3idxS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 24504.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: homo sapiens (human) |
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#2: Antibody | Mass: 23325.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: homo sapiens (human) |
#3: 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: 2.5 Å3/Da / Density % sol: 50.71 % |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 22% (w/v) PEG 4000, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2012 |
Radiation | Monochromator: SI 220. ROSENBAUM-ROCK DOUBLE- CRYSTAL MONOCHROMATOR: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 63455 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 11 % |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.3 % / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GBM, 3IDX Resolution: 1.6→35.4 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 26.55 / 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: 1.6→35.4 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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