Download MendeleyCryo-EM structure of SARS-CoV-2 receptor binding domain in complex with K202.B bispecific antibody
Yoo, Y., Cho, H.S.To be published.
7Y6K
Cryo-EM structure of SARS-CoV-2 receptor binding domain in complex with K202.B bispecific antibody
- PDB DOI: https://doi.org/10.2210/pdb7Y6K/pdb
- EM Map EMD-33642: EMDB EMDataResource
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Spodoptera frugiperda, Homo sapiens
- Mutation(s): Yes
- Deposited: 2022-06-20 Released: 2023-07-19
- Funding Organization(s): National Research Foundation (NRF, Korea)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.34 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Models: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike glycoprotein | A [auth B] | 1,208 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 9 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 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: P0DTC2-1 | ||||
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 |
| scFv region of light chain from K202.B, bispecific antibody | B [auth E], C [auth I] | 478 | 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 |
| Fab region of heavy chain from K202.B, bispecific antibody | D [auth J] | 454 | Homo sapiens | 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 Query on NAG | E [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.34 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | |
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| MODEL REFINEMENT | Coot | 0.9.8.1 |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Research Foundation (NRF, Korea) | Korea, Republic Of | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-07-19
Type: Initial release - Version 1.1: 2024-10-30
Changes: Data collection, Refinement description, Structure summary
