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Yorodumi- PDB-9fjk: Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fjk | ||||||
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Title | Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 | ||||||
Components |
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Keywords | VIRAL PROTEIN / Neutralizing Antibody / Conserved Epitope / Covid-19 / Spike | ||||||
Function / homology | Function and homology information virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Enterobacteria phage T4 (virus) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||
Authors | Bjoernsson, K.H. / Walker, M.R. / Raghavan, S.S.R. / Ward, A.B. / Barfod, L.K. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: To Be Published Title: Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 Authors: Bjoernsson, K.H. / Walker, M.R. / Raghavan, S.S.R. / Ward, A.B. / Barfod, L.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fjk.cif.gz | 656.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fjk.ent.gz | 531.9 KB | Display | PDB format |
PDBx/mmJSON format | 9fjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fjk_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 9fjk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 9fjk_validation.xml.gz | 103.7 KB | Display | |
Data in CIF | 9fjk_validation.cif.gz | 156.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/9fjk ftp://data.pdbj.org/pub/pdb/validation_reports/fj/9fjk | HTTPS FTP |
-Related structure data
Related structure data | 50503MC 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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1 |
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-Components
#1: Protein | Mass: 141481.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) Enterobacteria phage T4 (virus) Strain: BA.1 / Gene: S, 2, wac / Production host: Homo sapiens (human) / References: UniProt: P0DTC2, UniProt: P10104 #2: Antibody | | Mass: 14387.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | | Mass: 14002.314 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Details of virus | Empty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION | ||||||||||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: TBS, pH 7.5 | ||||||||||||||||||||||||||||
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 195000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Num. of particles selected: 591736 | ||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 87875 / Symmetry type: POINT |