8DV1
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432
- PDB DOI: https://doi.org/10.2210/pdb8DV1/pdb
- EM Map EMD-27730: EMDB EMDataResource
- Classification: VIRAL PROTEIN/ANTIVIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2022-07-27 Released: 2022-08-31
- Funding Organization(s): Department of Defense (DOD, United States), Chan Zuckerberg Initiative, Mercatus Center
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.40 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 2.3 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 glycoprotein | 1,208 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 5 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 |
| Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain | B [auth D] | 967 | Homo sapiens | Mutation(s): 4 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5 Go to UniProtKB: P0DOX5 | |||||
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1 | |||||
PHAROS: Q9BYF1 GTEx: ENSG00000130234 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | Q9BYF1P0DOX5 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | C [auth A] D E [auth D] F [auth D] G [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: 3.40 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-08-31 Deposition Author(s): QCRG Structural Biology Consortium, Remesh, S.G., Merz, G.E., Brilot, A.F., Chio, U., Verba, K.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Department of Defense (DOD, United States) | United States | HR0011-19-2-0020 |
| Chan Zuckerberg Initiative | United States | -- |
| Mercatus Center | United States | Emergent Ventures #2154 |
Revision History (Full details and data files)
- Version 1.0: 2022-08-31
Type: Initial release - Version 1.1: 2022-11-23
Changes: Database references - Version 2.0: 2022-11-30
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary - Version 2.1: 2023-03-01
Changes: Database references - Version 2.2: 2023-03-08
Changes: Database references - Version 2.3: 2023-03-15
Changes: Database references
