9YT4 | pdb_00009yt4

Local refinement of LP.8.1 spike (3-RBD-down), RBD-A and NTD-C

PDB DOI: https://doi.org/10.2210/pdb9YT4/pdb
EM Map EMD-73441: EMDB EMDataResource

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

Deposited: 2025-10-20 Released: 2026-06-17
Deposition Author(s): Wang, Y., Hu, Y., Chen, Z., Liang, B., Xie, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YT4

This is version 1.0 of the entry. See complete history.

Literature

Structural characteristics of the SARS-CoV-2 Omicron subvariant BA.3.2 and LP.8.1 spike protein

Wang, Y., Hu, Y., Chen, Z., Liang, B., Xie, X.

To be published.

Macromolecule Content

Total Structure Weight: 286.78 kDa
Atom Count: 4,229
Modeled Residue Count: 510
Deposited Residue Count: 2,566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 LP.8.1 spike	A [auth C], B [auth A]	1,283	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], D, E	2		N-Glycosylation	Interactions Focus chain C [auth B] Focus chain D Focus chain E Interactions & Density Focus chain C [auth B] Focus chain D Focus chain E

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth C]	F [auth C], G [auth C], H [auth C], I [auth A], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-06-17
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.