8HC4
SARS-CoV-2 wildtype spike trimer (6P) in complex with 3 YB9-258 Fabs and 3 R1-32 Fabs (3 RBD up)
- PDB DOI: https://doi.org/10.2210/pdb8HC4/pdb
- EM Map EMD-34651: EMDB EMDataResource
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2022-11-01 Released: 2023-01-25 
- Funding Organization(s): Other government
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.54 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. 
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): 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 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Heavy chain of R1-32 Fab | D, J [auth K], N | 228 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Light chain of R1-32 Fab | E, K [auth M], O | 214 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Heavy chain of YB9-258 | F, H, L [auth G] | 220 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Light chain of YB9-258 Fab | G [auth J], I [auth L], M [auth I] | 215 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | AA [auth a], P, Q, R, S, AA [auth a], P, Q, R, S, T, U, V, W, X, Y, Z | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG (Subject of Investigation/LOI) Query on NAG | AB [auth C] BA [auth A] BB [auth C] CA [auth A] CB [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.54 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | cryoSPARC |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-01-25  Deposition Author(s): Liu, B., Gao, X., Chen, Q., Li, Z., Su, M., He, J., Xiong, X.
Funding Organization | Location | Grant Number |
---|---|---|
Other government | EKPG21-06 | |
Other government | 2021A1515011289 | |
Other government | GRMH-GL |
Revision History (Full details and data files)
- Version 1.0: 2023-01-25
Type: Initial release - Version 1.1: 2023-05-03
Changes: Database references