9YPD | pdb_00009ypd

The ligand free HCoV-HKU1 spike structure obtained from data collected on 100 kV Tundra at 180kX magnification with Falcon C detector

PDB DOI: https://doi.org/10.2210/pdb9YPD/pdb
EM Map EMD-73294: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human coronavirus HKU1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-10-14 Released: 2026-10-21
Deposition Author(s): Pathirage, R., Acharya, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YPD

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

Literature

An integrated workflow for structural virology with a 100 keV electron microscope

Pathirage, R., Dutta, M., Acharya, P.

To be published.

Macromolecule Content

Total Structure Weight: 472.82 kDa
Atom Count: 29,516
Modeled Residue Count: 3,585
Deposited Residue Count: 4,071
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,357	Human coronavirus HKU1	Mutation(s): 0
UniProt
Find proteins for E0YJ44 (Human coronavirus HKU1) Explore E0YJ44 Go to UniProtKB: E0YJ44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E0YJ44
Glycosylation
Glycosylation Sites: 20	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

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	AA [auth a], D, DA [auth d], E, EA [auth e], AA [auth a], D, DA [auth d], E, EA [auth e], F, G, I, L, M, N, O, P, R, U, V, W, X, Y	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain D Focus chain DA [auth d] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain G Focus chain I Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain R Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain D Focus chain DA [auth d] Focus chain E Focus chain EA [auth e] Focus chain F Focus chain G Focus chain I Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain R Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, Q, Z	5		N-Glycosylation	Interactions Focus chain H Focus chain Q Focus chain Z Interactions & Density Focus chain H Focus chain Q Focus chain Z

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], J, K, S, BA [auth b], CA [auth c], J, K, S, T	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain J Focus chain K Focus chain S Focus chain T Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain J Focus chain K Focus chain S Focus chain T

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain FB [auth C] SDF format, chain HB [auth C] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth C] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain ZA [auth B] SDF format, chain YA [auth B] SDF format, chain XA [auth B] SDF format, chain WA [auth B] SDF format, chain VA [auth B] SDF format, chain RA [auth B] SDF format, chain OA [auth A] SDF format, chain LA [auth A] SDF format, chain KB [auth C] SDF format, chain KA [auth A] SDF format, chain IB [auth C] SDF format, chain HA [auth A] SDF format, chain GB [auth C] SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain EB [auth C] SDF format, chain BB [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain BB [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth C] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain KA [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain BB [auth C]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], IB [auth C], JA [auth A], JB [auth C], KA [auth A], KB [auth C], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21.2_5419:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI165947

Revision History (Full details and data files)

Version 1.0: 2026-10-21
Type: Initial release