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- PDB-5k6b: Crystal structure of prefusion-stabilized RSV F single-chain 9 DS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k6b | ||||||
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Title | Crystal structure of prefusion-stabilized RSV F single-chain 9 DS-Cav1 variant. | ||||||
![]() | Fusion glycoprotein F0 | ||||||
![]() | VIRAL PROTEIN / Respiratory Syncytial Virus / Prefusion / Vaccine / Stabilized | ||||||
Function / homology | ![]() positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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 / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joyce, M.G. / Zhang, B. / Rundlet, E.J. / Mascola, J.R. / Kwong, P.D. | ||||||
![]() | ![]() Title: Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV. Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / ...Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / Pancera, M. / Sastry, M. / Soto, C. / Stewart-Jones, G.B. / Thomas, P.V. / Van Galen, J.G. / Baxa, U. / Lee, K.K. / Mascola, J.R. / Graham, B.S. / Kwong, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191 KB | Display | ![]() |
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PDB format | ![]() | 153.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.7 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k6cC ![]() 5k6fC ![]() 5k6gC ![]() 5k6hC ![]() 5k6iC ![]() 4mmuS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: Protein | Mass: 49473.336 Da / Num. of mol.: 1 Fragment: UNP residues 26-105 linked to residues 145-509 via LINKER residues GS Source method: isolated from a genetically manipulated source Details: RSV F single-chain 9 DS-Cav1variant / Source: (gene. exp.) ![]() ![]() | ||
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#2: Sugar | ChemComp-NAG / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M NaOAc-Acetic Acid pH 5.5, 1.09 M Li2SO4, 0.12 M MgSO4, 3.33 % (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→28.94 Å / Num. obs: 17691 / % possible obs: 97.3 % / Redundancy: 4.3 % / Net I/σ(I): 11.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4mmu Resolution: 2.981→40.376 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.25 / 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: 2.981→40.376 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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