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

Validation slider image for 9R1Q

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2BW33
Glycosylation
Glycosylation Sites: 26	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, 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
Glycosylation Resources
GlyTouCan: G10756ZZ GlyCosmos: G10756ZZ GlyGen: G10756ZZ

Entity ID: 3
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	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
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
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	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
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
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)-[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]
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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]
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 11
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	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]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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 ZB [auth C] SDF format, chain ZA [auth A] SDF format, chain YB [auth C] SDF format, chain XB [auth C] SDF format, chain WB [auth C] SDF format, chain VB [auth C] SDF format, chain UB [auth C] SDF format, chain TB [auth C] SDF format, chain SB [auth B] SDF format, chain RB [auth B] SDF format, chain QB [auth B] SDF format, chain PB [auth B] SDF format, chain OB [auth B] SDF format, chain NB [auth B] SDF format, chain MB [auth B] SDF format, chain LB [auth B] SDF format, chain KB [auth B] SDF format, chain JB [auth B] SDF format, chain IB [auth A] SDF format, chain HB [auth A] SDF format, chain GB [auth A] SDF format, chain FB [auth A] SDF format, chain EB [auth A] SDF format, chain DB [auth A] SDF format, chain CC [auth C] SDF format, chain CB [auth A] SDF format, chain BC [auth C] SDF format, chain BB [auth A] SDF format, chain AC [auth C] SDF format, chain AB [auth A] MOL2 format, chain ZB [auth C] MOL2 format, chain ZA [auth A] MOL2 format, chain YB [auth C] MOL2 format, chain XB [auth C] MOL2 format, chain WB [auth C] MOL2 format, chain VB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain TB [auth C] MOL2 format, chain SB [auth B] MOL2 format, chain RB [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain OB [auth B] MOL2 format, chain NB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain IB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain CC [auth C] MOL2 format, chain CB [auth A] MOL2 format, chain BC [auth C] MOL2 format, chain BB [auth A] MOL2 format, chain AC [auth C] MOL2 format, chain AB [auth A] mmCIF format, chain ZB [auth C] mmCIF format, chain ZA [auth A] mmCIF format, chain YB [auth C] mmCIF format, chain XB [auth C] mmCIF format, chain WB [auth C] mmCIF format, chain VB [auth C] mmCIF format, chain UB [auth C] mmCIF format, chain TB [auth C] mmCIF format, chain SB [auth B] mmCIF format, chain RB [auth B] mmCIF format, chain QB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain OB [auth B] mmCIF format, chain NB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain IB [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain CC [auth C] mmCIF format, chain CB [auth A] mmCIF format, chain BC [auth C] mmCIF format, chain BB [auth A] mmCIF format, chain AC [auth C] mmCIF format, chain AB [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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

Hulswit, R.J.G.

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	101005077

Revision History (Full details and data files)

Version 1.0: 2026-02-11
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.