8ZHP

Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs

• PDB DOI: https://doi.org/10.2210/pdb8ZHP/pdb
• EM Map EMD-60111: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-05-11 Released: 2024-08-21 
• Deposition Author(s): Yan, Q., Gao, X., Liu, B., Hou, R., He, P., Li, Z., Chen, Q., Wang, J., He, J., Chen, L., Zhao, J., Xiong, X.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants

Yan, Q., Gao, X., Liu, B., Hou, R., He, P., Ma, Y., Zhang, Y., Zhang, Y., Li, Z., Chen, Q., Wang, J., Huang, X., Liang, H., Zheng, H., Yao, Y., Chen, X., Niu, X., He, J., Chen, L., Zhao, J., Xiong, X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A4B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 10-mer - A6B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 345.19 kDa 
• Atom Count: 22,856 
• Modelled Residue Count: 2,998 
• Deposited Residue Count: 3,188 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth C], F [auth A]	666	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of R1-32 Fab	B [auth D], G [auth B]	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of R1-32 Fab	C [auth E], H [auth F]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of H18 Fab	D [auth L], I	243	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of H18 Fab	E [auth H], J [auth G]	243	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	K [auth C], L [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Yan, Q., Gao, X., Liu, B., Hou, R., He, P., Li, Z., Chen, Q., Wang, J., He, J., Chen, L., Zhao, J., Xiong, X.

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Funding Organization	Location	Grant Number
Other government	China	2021A1515011289
Other government	China	SRPG22-002
Other government	China	EKPG21-06

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release