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- PDB-7sem: Structure-based design of prefusion-stabilized human metapneumovi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sem | |||||||||
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Title | Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins | |||||||||
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![]() | VIRAL PROTEIN/Immune System / human metapneumovirus / fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | |||||||||
Function / homology | Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rush, S.A. / Hsieh, C.-L. / McLellan, J.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins. Authors: Hsieh, C.L. / Rush, S.A. / Palomo, C. / Chou, C.W. / Pickens, W. / Mas, V. / McLellan, J.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.6 KB | Display | ![]() |
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PDB format | ![]() | 274.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.7 KB | Display | ![]() |
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Full document | ![]() | 485.4 KB | Display | |
Data in XML | ![]() | 32.2 KB | Display | |
Data in CIF | ![]() | 45.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sejC ![]() 5u68S ![]() 5wb0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23985.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Protein | Mass: 60357.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#3: Antibody | Mass: 22772.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 nl of the complex (5.4 mg/ml) with 50 nl of reservoir solution containing 10% (v/v) isopropanol, 0.1 M HEPES pH 7.5, and 20% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.95 Å / Num. obs: 54115 / % possible obs: 97.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 39.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.057 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4437 / CC1/2: 0.693 / Rpim(I) all: 0.542 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5wb0, 5u68 Resolution: 2.2→43.95 Å / SU ML: 0.2281 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2286 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 60.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.95 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 | Refine-ID: X-RAY DIFFRACTION
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