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Yorodumi- PDB-5u68: Structural basis for antibody cross-neutralization of respiratory... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u68 | ||||||
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Title | Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus | ||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / RSVF prefusion / MPE8 / cross-reactive antibody neutralization / Trimer / VIRAL PROTEIN-Immune System complex | ||||||
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 Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.083 Å | ||||||
Authors | Wen, X. / Jardetzky, T.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Microbiol / Year: 2017 Title: Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus. Authors: Wen, X. / Mousa, J.J. / Bates, J.T. / Lamb, R.A. / Crowe, J.E. / Jardetzky, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u68.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5u68.ent.gz | 965.4 KB | Display | PDB format |
PDBx/mmJSON format | 5u68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/5u68 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u68 | HTTPS FTP |
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-Related 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: 62452.488 Da / Num. of mol.: 3 Fragment: UNP P03420 residues 1-513,UNP M1E1E4 residues 1-28 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Human immunodeficiency virus 1 Strain: A2 / Plasmid: pTT5 / Cell line (production host): 293-6E / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: M1E1E4 #2: Antibody | Mass: 30684.664 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: single chain antibody (scFv) / Source: (gene. exp.) Homo sapiens (human) / 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: 3.45 Å3/Da / Density % sol: 64.36 % / Description: rod-shaped |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Potassium Nitrate, 0.1M Citrate Phosphate pH 4.2, 1 % Tacsimate pH 7.0, 14 (w/v) % PEG 6000 PH range: 7.0-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 13, 2015 / Details: Fibre Optic Taper (FOT) |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.191 Å / Num. obs: 71891 / % possible obs: 99.98 % / Redundancy: 11.2 % / Net I/σ(I): 11.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JHW, 3H42 Resolution: 3.083→48.191 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9 / 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: 3.083→48.191 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -135.4741 Å / Origin y: 162.3403 Å / Origin z: 288.1867 Å
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Refinement TLS group | Selection details: all |