Download MendeleyCryo-EM map of SARS-CoV-2 Omicron BA.2 spike in complex with 2130-1-0114-112
Binshtein, E., Crowe, J.E.To be published.
8EKD
Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike in complex with 2130-1-0114-112
- PDB DOI: https://doi.org/10.2210/pdb8EKD/pdb
- EM Map EMD-28199: EMDB EMDataResource
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2022-09-20 Released: 2024-02-21
- Funding Organization(s): Defense Advanced Research Projects Agency (DARPA), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.60 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
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
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Fab LLNL-199 HC | A [auth E] | 131 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Fab LLNL-199 LC | B [auth F] | 113 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike protein S2' | C [auth G] | 184 | Severe acute respiratory syndrome coronavirus | Mutation(s): 0 Gene Names: S, 2 |  |
UniProt | |||||
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTC2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG (Subject of Investigation/LOI) Query on NAG | D [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.60 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | RELION | 4 |
| MODEL REFINEMENT | PHENIX |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-02-21 Deposition Author(s): Binshtein, E., Crowe, J.E.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Defense Advanced Research Projects Agency (DARPA) | United States | HR0011-18-3-0001 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI157155 |
Revision History (Full details and data files)
- Version 1.0: 2024-02-21
Type: Initial release - Version 1.1: 2024-03-13
Changes: Database references, Structure summary
