[English] 日本語
Yorodumi- PDB-8r8k: XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r8k | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein | |||||||||||||||
Components |
| |||||||||||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / Spike / Glycoprotein / Coronavirus / antibody / Fab / XBB.1.5 / therapeutic / complex / neutralising / RBD / receptor binding domain / convalescent sera / immune system / XBB-4 / BA.2.12.1 / omicron variant / virus / BA.2.86 | |||||||||||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||||||||
Authors | Duyvesteyn, H.M.E. / Ren, J. / Stuart, D.I. | |||||||||||||||
Funding support | United Kingdom, 4items
| |||||||||||||||
Citation | Journal: To Be Published Title: The emerging BA.2.86 Omicron sub-lineage balances antibody escape and ACE2 affinity Authors: Liu, C. / Zhou, D. / Duyvesteyn, H.M.E. / Fry, E.E. / Ren, J. / Stuart, D.I. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8r8k.cif.gz | 139 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8r8k.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 8r8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/8r8k ftp://data.pdbj.org/pub/pdb/validation_reports/r8/8r8k | HTTPS FTP |
---|
-Related structure data
Related structure data | 19002MC 8qrfC 8qrgC 8qsqC 8qtdC 8r80C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 142729.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Homo sapiens (human) / References: UniProt: A0A7L9WCR1 |
---|---|
#2: Antibody | Mass: 24755.660 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: 23185.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| ||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Spike ectodomain incubated with XBB-4 Fab in 2-fold molecular excess of sites (assuming three per trimeric spike unit). | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.5 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / Calibrated magnification: 165000 X / Nominal defocus max: 2700 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) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: Patch CTF and Motion correction, on-the-fly. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3282771 / Details: Blob picker in cryoSPARC live interface. | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61333 Details: Determined by cryoSPARC. Local refinement job centred around one fab and RBD. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8CIM Accession code: 8CIM / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||
Refine LS restraints |
|