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Yorodumi- PDB-8u1q: A mechanistic understanding of protective influenza B neuraminida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u1q | ||||||
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Title | A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface | ||||||
Components |
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Keywords | HYDROLASE / Neuraminidase Sialidase | ||||||
Function / homology | Function and homology information : / : / : / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza B virus Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||
Authors | Ferguson, J.A. / Oeverdieck, S. / Ward, A.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface Authors: Ferguson, J.A. / Oeverdieck, S. / Ward, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u1q.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u1q.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 8u1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u1q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8u1q_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8u1q_validation.xml.gz | 31 KB | Display | |
Data in CIF | 8u1q_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/8u1q ftp://data.pdbj.org/pub/pdb/validation_reports/u1/8u1q | HTTPS FTP |
-Related structure data
Related structure data | 41824MC 8u1cC 8u1sC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: C4 (4 fold cyclic)) |
-Components
#1: Protein | Mass: 51104.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Iowa/06/2017) / Gene: NA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): D2 / References: UniProt: A0A1S7DL21 |
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#2: Antibody | Mass: 13139.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) |
#3: Antibody | Mass: 11627.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of human mAb-fv domain bound to influenza B neuraminidase, from a public database. Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||||||||
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||
Source (recombinant) |
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Buffer solution | pH: 7.4 / Details: TBS | ||||||||||||||||||
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Calibrated magnification: 36000 X / Nominal defocus max: 700 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 50.43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2559 |
Image scans | Width: 4048 / Height: 4048 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335369 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.01 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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