7NLL
SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies
- PDB DOI: https://doi.org/10.2210/pdb7NLL/pdb
- EM Map EMD-12465: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): No
- Deposited: 2021-02-22 Released: 2022-02-02
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.89 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 2.0 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike protein S1 | A [auth B], B [auth D] | 230 | Severe acute respiratory syndrome coronavirus 2 | 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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nanobody Fu2 | C [auth A], D [auth C] | 145 | Vicugna pacos | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 | E [auth B], F [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.89 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | 1.19 |
| RECONSTRUCTION | cryoSPARC | 3.0.1 |
Entry History
Deposition Data
- Released Date: 2022-02-02 Deposition Author(s): Das, H., Hallberg, B.M.
Revision History (Full details and data files)
- Version 1.0: 2022-02-02
Type: Initial release - Version 2.0: 2023-09-27
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
