[English] 日本語
Yorodumi- PDB-8u1c: A mechanistic understanding of protective influenza B neuraminida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u1c | ||||||
---|---|---|---|---|---|---|---|
Title | A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface | ||||||
Components |
| ||||||
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 | Homo sapiens (human) Influenza B virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
Authors | Ferguson, J.A. / Oeverdieck, S. / Ward, A.B. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8u1c.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8u1c.ent.gz | 97.5 KB | Display | PDB format |
PDBx/mmJSON format | 8u1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u1c_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8u1c_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8u1c_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 8u1c_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/8u1c ftp://data.pdbj.org/pub/pdb/validation_reports/u1/8u1c | HTTPS FTP |
-Related structure data
Related structure data | 41809MC 8u1qC 8u1sC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
2 |
|
3 |
|
Symmetry | Point symmetry: (Schoenflies symbol: C4 (4 fold cyclic)) |
-Components
#1: Antibody | Mass: 14438.196 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) |
---|---|
#2: Antibody | Mass: 11529.794 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: 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 / Cell line (production host): D2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A1S7DL21 |
#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 |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of human donor mAb-fv domain bound to influenza B neuraminidase Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||
Source (natural) |
| ||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||
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 | ||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||
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 |
---|---|
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: 190000 X / Calibrated magnification: 190000 X / Nominal defocus max: 700 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 49.87 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5958 |
Image scans | Width: 4048 / Height: 4048 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1096437 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220989 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.06 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|