+Open data
-Basic information
Entry | Database: PDB / ID: 8qtd | |||||||||
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Title | Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Viral protein/immune system / SARS-CoV-2 / XBB-7 / RBD / Spike / BA.2.86 | |||||||||
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 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Ren, J. / Duyvesteyn, H.M.E. / Stuart, D.I. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: The emerging BA.2.86 Omicron sub-lineage balances antibody escape and ACE2 affinity Authors: Stuart, D.I. / Liu, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qtd.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qtd.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 8qtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/8qtd ftp://data.pdbj.org/pub/pdb/validation_reports/qt/8qtd | HTTPS FTP |
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-Related structure data
Related structure data | 18649MC 8qrfC 8qrgC 8qsqC 8r80C 8r8kC 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: 142385.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2, wac / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0DTC2, UniProt: P10104 |
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#2: Antibody | Mass: 14613.259 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 10388.351 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
-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 |
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Source (natural) |
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Source (recombinant) |
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Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: BA-2.86 Spike with XBB-7 fab in 6-fold excess of S protein. | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9664 / Details: Images were collected in EER format. |
-Processing
EM software |
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CTF correction | Details: Determined using cryoSPARC live patch CTF correction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 524958 | |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75021 / Details: Determined by cryoSPARC. / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: Phenix real space refinement with manual checks using coot. | |||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8CIM Accession code: 8CIM / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||
Refine LS restraints |
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