9R1Q | pdb_00009r1q

Beluga whale coronavirus spike glycoprotein

PDB DOI: https://doi.org/10.2210/pdb9R1Q/pdb
EM Map EMD-53512: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Beluga whale coronavirus SW1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-04-28 Released: 2026-02-11
Deposition Author(s): Hulswit, R.J.G., Hurdiss, D.L.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.24 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

Atypical features of cetacean coronavirus spikes highlight structural plasticity of the S glycoprotein

Hulswit, R.J.G., Hurdiss, D.L.

To be published.

Macromolecule Content

Total Structure Weight: 503.42 kDa
Atom Count: 32,256
Modeled Residue Count: 3,777
Deposited Residue Count: 4,131
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein	A, B, C	1,377	Beluga whale coronavirus SW1	Mutation(s): 0
UniProt
Find proteins for B2BW33 (Beluga whale coronavirus (strain SW1)) Explore B2BW33 Go to UniProtKB: B2BW33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2BW33
Glycosylation
Glycosylation Sites: 26	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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, JA [auth j], T	5		N-Glycosylation	Interactions Focus chain D Focus chain JA [auth j] Focus chain T Interactions & Density Focus chain D Focus chain JA [auth j] Focus chain T

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I, KA [auth k], MA [auth m], E, G, I, KA [auth k], MA [auth m], OA [auth o], U, W, Y	3		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain I Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain U Focus chain W Focus chain Y Interactions & Density Focus chain E Focus chain G Focus chain I Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain U Focus chain W Focus chain Y

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	AA [auth a], H, K, NA [auth n], QA [auth q], AA [auth a], H, K, NA [auth n], QA [auth q], X	4		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain H Focus chain K Focus chain NA [auth n] Focus chain QA [auth q] Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain H Focus chain K Focus chain NA [auth n] Focus chain QA [auth q] Focus chain X

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	J, PA [auth p], Z	5		N-Glycosylation	Interactions Focus chain J Focus chain PA [auth p] Focus chain Z Interactions & Density Focus chain J Focus chain PA [auth p] Focus chain Z

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], EA [auth e], GA [auth g], L, O, BA [auth b], EA [auth e], GA [auth g], L, O, Q, RA [auth r], UA [auth u], WA [auth w]	6		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain L Focus chain O Focus chain Q Focus chain RA [auth r] Focus chain UA [auth u] Focus chain WA [auth w] Interactions & Density Focus chain BA [auth b] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain L Focus chain O Focus chain Q Focus chain RA [auth r] Focus chain UA [auth u] Focus chain WA [auth w]

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], IA [auth i], M, S, SA [auth s], CA [auth c], IA [auth i], M, S, SA [auth s], YA [auth y]	2		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain IA [auth i] Focus chain M Focus chain S Focus chain SA [auth s] Focus chain YA [auth y] Interactions & Density Focus chain CA [auth c] Focus chain IA [auth i] Focus chain M Focus chain S Focus chain SA [auth s] Focus chain YA [auth y]

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], N, TA [auth t]	4		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain N Focus chain TA [auth t] Interactions & Density Focus chain DA [auth d] Focus chain N Focus chain TA [auth t]

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f], P, VA [auth v]	2		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain P Focus chain VA [auth v] Interactions & Density Focus chain FA [auth f] Focus chain P Focus chain VA [auth v]

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], R, XA [auth x]	3		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain R Focus chain XA [auth x] Interactions & Density Focus chain HA [auth h] Focus chain R Focus chain XA [auth x]

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 A] SDF format, chain AC [auth C] SDF format, chain BB [auth A] SDF format, chain BC [auth C] SDF format, chain CB [auth A] SDF format, chain CC [auth C] SDF format, chain DB [auth A] SDF format, chain FB [auth A] SDF format, chain GB [auth A] SDF format, chain HB [auth A] SDF format, chain IB [auth A] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain NB [auth B] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain QB [auth B] SDF format, chain RB [auth B] SDF format, chain SB [auth B] SDF format, chain TB [auth C] SDF format, chain UB [auth C] SDF format, chain VB [auth C] SDF format, chain WB [auth C] SDF format, chain XB [auth C] SDF format, chain YB [auth C] SDF format, chain ZA [auth A] SDF format, chain ZB [auth C] SDF format, chain EB [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth C] MOL2 format, chain BB [auth A] MOL2 format, chain BC [auth C] MOL2 format, chain CB [auth A] MOL2 format, chain CC [auth C] MOL2 format, chain DB [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain NB [auth B] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain RB [auth B] MOL2 format, chain SB [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain VB [auth C] MOL2 format, chain WB [auth C] MOL2 format, chain XB [auth C] MOL2 format, chain YB [auth C] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth C] MOL2 format, chain EB [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain AC [auth C] mmCIF format, chain BB [auth A] mmCIF format, chain BC [auth C] mmCIF format, chain CB [auth A] mmCIF format, chain CC [auth C] mmCIF format, chain DB [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain IB [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain NB [auth B] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain QB [auth B] mmCIF format, chain RB [auth B] mmCIF format, chain SB [auth B] mmCIF format, chain TB [auth C] mmCIF format, chain UB [auth C] mmCIF format, chain VB [auth C] mmCIF format, chain WB [auth C] mmCIF format, chain XB [auth C] mmCIF format, chain YB [auth C] mmCIF format, chain ZA [auth A] mmCIF format, chain ZB [auth C] mmCIF format, chain EB [auth A]	AB [auth A] AC [auth C] BB [auth A] BC [auth C] CB [auth A] AB [auth A], AC [auth C], BB [auth A], BC [auth C], CB [auth A], CC [auth C], DB [auth A], EB [auth A], FB [auth A], GB [auth A], HB [auth A], IB [auth A], JB [auth B], KB [auth B], LB [auth B], MB [auth B], NB [auth B], OB [auth B], PB [auth B], QB [auth B], RB [auth B], SB [auth B], TB [auth C], UB [auth C], VB [auth C], WB [auth C], XB [auth C], YB [auth C], ZA [auth A], ZB [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain AC [auth C] Focus chain BB [auth A] Focus chain BC [auth C] Focus chain CB [auth A] Focus chain CC [auth C] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SB [auth B] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C] Focus chain ZA [auth A] Focus chain ZB [auth C] Interactions & Density Focus chain AB [auth A] Focus chain AC [auth C] Focus chain BB [auth A] Focus chain BC [auth C] Focus chain CB [auth A] Focus chain CC [auth C] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SB [auth B] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C] Focus chain ZA [auth A] Focus chain ZB [auth C]