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- PDB-6i9i: Rift valley fever virus Gn in complex with a neutralizing antibod... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i9i | |||||||||
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Title | Rift valley fever virus Gn in complex with a neutralizing antibody fragment | |||||||||
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![]() | VIRAL PROTEIN / Glycoprotein / Antibody / phlebovirus / neutralization | |||||||||
Function / homology | ![]() host cell mitochondrial outer membrane / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / virion component => GO:0044423 / host cell Golgi membrane / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane ...host cell mitochondrial outer membrane / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / virion component => GO:0044423 / host cell Golgi membrane / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Allen, E.R. / Bowden, T.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A Protective Monoclonal Antibody Targets a Site of Vulnerability on the Surface of Rift Valley Fever Virus. Authors: Allen, E.R. / Krumm, S.A. / Raghwani, J. / Halldorsson, S. / Elliott, A. / Graham, V.A. / Koudriakova, E. / Harlos, K. / Wright, D. / Warimwe, G.M. / Brennan, B. / Huiskonen, J.T. / Dowall, ...Authors: Allen, E.R. / Krumm, S.A. / Raghwani, J. / Halldorsson, S. / Elliott, A. / Graham, V.A. / Koudriakova, E. / Harlos, K. / Wright, D. / Warimwe, G.M. / Brennan, B. / Huiskonen, J.T. / Dowall, S.D. / Elliott, R.M. / Pybus, O.G. / Burton, D.R. / Hewson, R. / Doores, K.J. / Bowden, T.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 387.5 KB | Display | ![]() |
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PDB format | ![]() | 311.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4j02S 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Antibody | Mass: 23616.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 22819.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 36075.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 500, 0.1 M bis-Tris pH 6.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→23.6 Å / Num. obs: 59882 / % possible obs: 96.2 % / Redundancy: 1.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.072 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.98→2.03 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.67 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J02 Resolution: 1.98→23.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.777 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.972 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→23.6 Å
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Refine LS restraints |
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