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Yorodumi- PDB-4zyp: Crystal Structure of Motavizumab and Quaternary-Specific RSV-Neut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zyp | ||||||
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Title | Crystal Structure of Motavizumab and Quaternary-Specific RSV-Neutralizing Human Antibody AM14 in Complex with Prefusion RSV F Glycoprotein | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig domain / Fab / fusion / respiratory syncytial virus / prefusion | ||||||
Function / homology | Function and homology information positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus A Enterobacteria phage T4 (virus) Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.5 Å | ||||||
Authors | Gilman, M.S.A. / McLellan, J.S. | ||||||
Citation | Journal: Plos Pathog. / Year: 2015 Title: Characterization of a Prefusion-Specific Antibody That Recognizes a Quaternary, Cleavage-Dependent Epitope on the RSV Fusion Glycoprotein. Authors: Gilman, M.S. / Moin, S.M. / Mas, V. / Chen, M. / Patel, N.K. / Kramer, K. / Zhu, Q. / Kabeche, S.C. / Kumar, A. / Palomo, C. / Beaumont, T. / Baxa, U. / Ulbrandt, N.D. / Melero, J.A. / ...Authors: Gilman, M.S. / Moin, S.M. / Mas, V. / Chen, M. / Patel, N.K. / Kramer, K. / Zhu, Q. / Kabeche, S.C. / Kumar, A. / Palomo, C. / Beaumont, T. / Baxa, U. / Ulbrandt, N.D. / Melero, J.A. / Graham, B.S. / McLellan, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zyp.cif.gz | 678.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zyp.ent.gz | 565.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/4zyp ftp://data.pdbj.org/pub/pdb/validation_reports/zy/4zyp | HTTPS FTP |
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-Related structure data
Related structure data | 4zykSC 3ixtS 4jhwS 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: Protein | Mass: 55120.879 Da / Num. of mol.: 3 / Mutation: S155C, S190F, V207L, S290C, I379V, M447V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Enterobacteria phage T4 (virus) Strain: A2 / Plasmid: p(alpha)H / Gene: wac, T4Tp161 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: D9IEJ2 #2: Antibody | Mass: 24284.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Humanized mouse antibody / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #3: Antibody | Mass: 23150.730 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Humanized mouse antibody / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pVRC8400 / Production host: Homo sapiens (human) #4: Antibody | Mass: 24365.150 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #5: Antibody | Mass: 23615.227 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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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: 3.1 Å3/Da / Density % sol: 60.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5.645mg/mL EndoH digested DS-Cav1 + AM14 Fab + Motavizumab Fab, 11.4% PEG8000, 1.71% MPD, 0.1M Imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 5.5→49.59 Å / Num. obs: 17434 / % possible obs: 97.5 % / Redundancy: 3 % / Biso Wilson estimate: 161.85 Å2 / CC1/2: 0.939 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.125 / Net I/σ(I): 4.8 / Num. measured all: 51879 / Scaling rejects: 33 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JHW, 3IXT, 4ZYK Resolution: 5.5→49.386 Å / SU ML: 0.91 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.56 / 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: 5.5→49.386 Å
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Refine LS restraints |
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LS refinement shell |
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