Structure of scFv76 in complex with SARS-CoV-2 Omicron Spike protein
Chaves-Sanjuan, A., Bolognesi, M.To be published.
9FGT
SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76 (focused refinement)
- PDB DOI: https://doi.org/10.2210/pdb9FGT/pdb
- EM Map EMD-50424: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, Homo sapiens
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): Yes
- Deposited: 2024-05-25 Released: 2024-06-12
- Funding Organization(s): Other private
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.80 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| Spike glycoprotein,Fibritin | A [auth C] | 1,214 | Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4 This entity is chimeric | Mutation(s): 35 Gene Names: S, 2, wac | |
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2 | |||||
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104 Go to UniProtKB: P10104 | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | P0DTC2P10104 | ||||
| Glycosylation Sites: 1 | Go to GlyGen: P0DTC2-1 | ||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| Single chain fragment scFv76 | B [auth E] | 264 | Homo sapiens | Mutation(s): 0 | |
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | C | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.80 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | |
| RECONSTRUCTION | cryoSPARC | 3.3.1 |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-06-12 Deposition Author(s): Berlinguer, M., Chaves-Sanjuan, A., Milazzo, F.M., Minenkova, O., De Santis, R., Bolognesi, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other private | Italy | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-06-12
Type: Initial release - Version 1.1: 2024-11-20
Changes: Data collection, Structure summary