+Open data
-Basic information
Entry | Database: PDB / ID: 6dc3 | ||||||
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Title | RSV prefusion F bound to RSD5 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Viral glycoprotein / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway ...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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / 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 / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human respiratory syncytial virus A Human immunodeficiency virus 1 unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.501 Å | ||||||
Authors | Battles, M.B. / McLellan, J.S. / Jones, H.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos Pathog. / Year: 2019 Title: Alternative conformations of a major antigenic site on RSV F. Authors: Jones, H.G. / Battles, M.B. / Lin, C.C. / Bianchi, S. / Corti, D. / 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 | 6dc3.cif.gz | 368.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dc3.ent.gz | 302.4 KB | Display | PDB format |
PDBx/mmJSON format | 6dc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/6dc3 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/6dc3 | HTTPS FTP |
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-Related structure data
Related structure data | 6dc4C 6dc5C 1dfbS 1mcoS 4mmuS 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: 24454.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6N089 | ||
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#2: Antibody | Mass: 22819.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8N355 | ||
#3: Protein | Mass: 63218.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Human immunodeficiency virus 1, (gene. exp.) unidentified (others) Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: M1E1E4 | ||
#4: Chemical | ChemComp-SO4 / #5: Sugar | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.88 Å3/Da / Density % sol: 84.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Lithium sulfate, 0.1 M Tris pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2015 | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→38.23 Å / Num. obs: 41327 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 126.75 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.053 / Rrim(I) all: 0.117 / Net I/σ(I): 9.7 / Num. measured all: 198500 / Scaling rejects: 205 | |||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MMU, 1DFB, 1MCO Resolution: 3.501→38.229 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.91 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 315.77 Å2 / Biso mean: 132.1736 Å2 / Biso min: 59.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.501→38.229 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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