9OW6 | pdb_00009ow6

Hedgehog coronavirus ErinCoV-Ger12 spike receptor binding domain in complex with hedgehog APN

PDB DOI: https://doi.org/10.2210/pdb9OW6/pdb
EM Map EMD-70930: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Erinaceus europaeus, Streptomyces, Betacoronavirus Erinaceus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-06-02 Released: 2026-07-08
Deposition Author(s): Jin, M., Rini, J.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Hedgehog coronavirus ErinCoV-Ger12 spike receptor binding domain in complex with hedgehog APN

Jin, M., Rini, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 262.28 kDa
Atom Count: 18,522
Modeled Residue Count: 2,226
Deposited Residue Count: 2,228
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A, D	900	Erinaceus europaeus	Mutation(s): 0 Gene Names: ANPEP EC: 3.4.11
UniProt
Find proteins for A0A1S2ZAK1 (Erinaceus europaeus) Explore A0A1S2ZAK1 Go to UniProtKB: A0A1S2ZAK1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1S2ZAK1
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A Focus chain D
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Amastatin	B, E	4	Streptomyces	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C, F	210	Betacoronavirus Erinaceus	Mutation(s): 0
UniProt
Find proteins for U5LMM7 (Betacoronavirus Erinaceus/VMC/DEU/2012) Explore U5LMM7 Go to UniProtKB: U5LMM7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U5LMM7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	G, H, I, J, M G, H, I, J, M, N, O, P, Q, R, U, V	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain U Focus chain V Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain U Focus chain V

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

Entity ID: 6
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	L, T	3		N-Glycosylation	Interactions Focus chain L Focus chain T Interactions & Density Focus chain L Focus chain T

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain EA [auth D] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] SDF format, chain FA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain FA [auth D] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain FA [auth D]	AA [auth A] BA [auth D] CA [auth D] EA [auth D] FA [auth D] AA [auth A], BA [auth D], CA [auth D], EA [auth D], FA [auth D], W [auth A], X [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain Y [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain Y [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain Y [auth A]	DA [auth D], Y [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain Y [auth A] Interactions & Density Focus chain DA [auth D] Focus chain Y [auth A]