43YY | pdb_000043yy

Cryo-EM structure of N19 Fab : D0D-S1A

PDB DOI: https://doi.org/10.2210/pdb43YY/pdb
EM Map EMD-82402: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Porcine epidemic diarrhea virus, Sus scrofa
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-07-22 Released: 2026-08-05
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: 2.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 43YY

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: 84.31 kDa
Atom Count: 5,020
Modeled Residue Count: 638
Deposited Residue Count: 760
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	487	Porcine epidemic diarrhea virus	Mutation(s): 0 Gene Names: S
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: 5	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N19 VH	B [auth H]	144	Sus scrofa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N19 VL	C [auth L]	129	Sus scrofa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 5
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	E [auth C]	5		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

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 F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [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 F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.30 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: 2026-08-05

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: 2026-08-05
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.