Download MendeleyCryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
Zhang, Z., Ju, B., Liu, C.To be published.
9LBS | pdb_00009lbs
Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
- PDB DOI: https://doi.org/10.2210/pdb9LBS/pdb
- EM Map EMD-62955: EMDB EMDataResource
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
- Expression System: Homo sapiens
- Mutation(s): Yes
- Deposited: 2025-01-03 Released: 2025-04-02
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.41 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Models: experimental, in silico
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Heavy chain of S309 Fab | 126 | Homo sapiens | Mutation(s): 0 |  | |
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| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Light chain of S309 Fab | 107 | Homo sapiens | Mutation(s): 0 |  | |
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| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Heavy chain of S304 Fab | C [auth H] | 119 | Homo sapiens | Mutation(s): 0 |  |
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| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Light chain of S304 Fab | D [auth L] | 108 | Homo sapiens | Mutation(s): 0 |  |
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| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Heavy chain of ConBA-998 | E [auth D] | 118 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike protein S1 | 181 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 16 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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Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Light chain of ConBA-998 | G [auth C] | 108 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | H [auth E] | 3 |  | N-Glycosylation | |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.41 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | |
| MODEL REFINEMENT | PHENIX | 1.20.1_4487 |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 82025022 |
Revision History (Full details and data files)
- Version 1.0: 2025-04-02
Type: Initial release
