9XNZ | pdb_00009xnz

PEDV HNXX spike trimer with three D0 up

PDB DOI: https://doi.org/10.2210/pdb9XNZ/pdb
EM Map EMD-67064: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Porcine epidemic diarrhea virus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-11-13 Released: 2026-08-26
Deposition Author(s): Liu, J., Wang, S., Wang, J., Su, M., Li, Z., Xiong, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9XNZ

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

Literature

Locking Spike Domain 0 Conformation Impairs Fusion and Neutralizes Porcine Epidemic Diarrhea Virus

Wang, S., Liu, J.B., Wang, J.J., Su, M.Z., Li, Z.M., Wang, Z.C., Ma, Y., Li, Y., Liu, B.H., Zou, J.H., Zhu, X.R., Habib, G., Cheng, Y.Q., Li, H.Y., Zhou, M., Li, M., Liu, Y.T., He, J., Xiao, S.B., Li, W.T., Chen, X.W., Zhou, H.B., Xiong, X.L.

To be published.

Macromolecule Content

Total Structure Weight: 452.11 kDa
Atom Count: 27,378
Modeled Residue Count: 3,423
Deposited Residue Count: 3,981
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,327	Porcine epidemic diarrhea virus	Mutation(s): 0
UniProt
Find proteins for A0A7G4RNN0 (Porcine epidemic diarrhea virus) Explore A0A7G4RNN0 Go to UniProtKB: A0A7G4RNN0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7G4RNN0
Glycosylation
Glycosylation Sites: 18	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
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	D, G, J	5		N-Glycosylation	Interactions Focus chain D Focus chain G Focus chain J Interactions & Density Focus chain D Focus chain G Focus chain J

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, H, I, K E, F, H, I, K, L	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAM Query on PAM Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain RA [auth B] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain VA [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain VA [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain VA [auth B]	DA [auth A] EA [auth A] RA [auth B] VA [auth B] Y [auth A] DA [auth A], EA [auth A], RA [auth B], VA [auth B], Y [auth A], Z [auth A]	PALMITOLEIC ACID C₁₆ H₃₀ O₂ SECPZKHBENQXJG-FPLPWBNLSA-N		Interactions Focus chain DA [auth A] Focus chain EA [auth A] Focus chain RA [auth B] Focus chain VA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain DA [auth A] Focus chain EA [auth A] Focus chain RA [auth B] Focus chain VA [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth C] SDF format, chain CA [auth A] SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain XA [auth C] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain X [auth A] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain Q [auth A] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain KA [auth B] SDF format, chain GB [auth C] SDF format, chain GA [auth B] SDF format, chain FB [auth C] SDF format, chain EB [auth C] SDF format, chain DB [auth C] SDF format, chain CB [auth C] SDF format, chain BB [auth C] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain BA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain BA [auth A]	AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [auth A] AA [auth A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], DB [auth C], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], W [auth A], WA [auth C], X [auth A], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82341085

Revision History (Full details and data files)

Version 1.0: 2026-08-26
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.