9UEL | pdb_00009uel

Local refinement of NTD and RBD domains of SARS-CoV2 KP.3.1.1 spike protein

PDB DOI: https://doi.org/10.2210/pdb9UEL/pdb
EM Map EMD-64085: EMDB EMDataResource

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

Deposited: 2025-04-08 Released: 2025-11-12
Deposition Author(s): He, M.Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UEL

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

Literature

Intrinsic pathogenicity, virological features, and immune evasion of SARS-CoV-2 JN.1-derived variants including JN.1.7, KP.2, KP.3, and KP.3.1.1

He, M.Z.

To be published.

Macromolecule Content

Total Structure Weight: 146.15 kDa
Atom Count: 4,485
Modeled Residue Count: 576
Deposited Residue Count: 1,305
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV2 KP.3.1.1 spike glycoprotein	A	1,305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0

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 B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain C [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32401012

Revision History (Full details and data files)

Version 1.0: 2025-11-12
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.