9R1R | pdb_00009r1r

Bottlenose dolphin coronavirus spike glycoprotein

PDB DOI: https://doi.org/10.2210/pdb9R1R/pdb
EM Map EMD-53513: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Bottlenose dolphin coronavirus HKU22
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-04-28 Released: 2026-01-14
Deposition Author(s): Hulswit, R.J.G., Hurdiss, D.L.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 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: 492.31 kDa
Atom Count: 31,461
Modeled Residue Count: 3,663
Deposited Residue Count: 4,044
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 glycoprotein	A, B, C	1,348	Bottlenose dolphin coronavirus HKU22	Mutation(s): 0
UniProt
Find proteins for V5TEW2 (Bottlenose dolphin coronavirus HKU22) Explore V5TEW2 Go to UniProtKB: V5TEW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V5TEW2
Glycosylation
Glycosylation Sites: 31	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AB [auth 0], CA [auth c], D, EA [auth e], FA [auth f], AB [auth 0], CA [auth c], D, EA [auth e], FA [auth f], GA [auth g], HA [auth h], J, L, M, N, O, PA [auth p], VA [auth v], W, XA [auth x], YA [auth y], ZA [auth z]	3		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain D Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain PA [auth p] Focus chain VA [auth v] Focus chain W Focus chain XA [auth x] Focus chain YA [auth y] Focus chain ZA [auth z] Interactions & Density Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain D Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain PA [auth p] Focus chain VA [auth v] Focus chain W Focus chain XA [auth x] Focus chain YA [auth y] Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], DB [auth 3], E, EB [auth 4], AA [auth a], BA [auth b], DB [auth 3], E, EB [auth 4], F, G, GB [auth 6], H, HB [auth 7], I, KA [auth k], LA [auth l], NA [auth n], OA [auth o], QA [auth q], R, RA [auth r], S, SA [auth s], TA [auth t], U, UA [auth u], V, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DB [auth 3] Focus chain E Focus chain EB [auth 4] Focus chain F Focus chain G Focus chain GB [auth 6] Focus chain H Focus chain HB [auth 7] Focus chain I Focus chain KA [auth k] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DB [auth 3] Focus chain E Focus chain EB [auth 4] Focus chain F Focus chain G Focus chain GB [auth 6] Focus chain H Focus chain HB [auth 7] Focus chain I Focus chain KA [auth k] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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)-2-acetamido-2-deoxy-beta-D-glucopyranose	CB [auth 2], DA [auth d], JA [auth j], K, Q, CB [auth 2], DA [auth d], JA [auth j], K, Q, WA [auth w]	4		N-Glycosylation	Interactions Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain JA [auth j] Focus chain K Focus chain Q Focus chain WA [auth w] Interactions & Density Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain JA [auth j] Focus chain K Focus chain Q Focus chain WA [auth w]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 5
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	BB [auth 1], IA [auth i], P	5		N-Glycosylation	Interactions Focus chain BB [auth 1] Focus chain IA [auth i] Focus chain P Interactions & Density Focus chain BB [auth 1] Focus chain IA [auth i] Focus chain P
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	FB [auth 5], MA [auth m], T	6		N-Glycosylation	Interactions Focus chain FB [auth 5] Focus chain MA [auth m] Focus chain T Interactions & Density Focus chain FB [auth 5] Focus chain MA [auth m] Focus chain T
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

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 AC [auth B] SDF format, chain BC [auth B] SDF format, chain CC [auth B] SDF format, chain DC [auth B] SDF format, chain EC [auth B] SDF format, chain FC [auth B] SDF format, chain GC [auth C] SDF format, chain HC [auth C] SDF format, chain IB [auth A] SDF format, chain IC [auth C] SDF format, chain JB [auth A] SDF format, chain JC [auth C] SDF format, chain KB [auth A] SDF format, chain KC [auth C] SDF format, chain LB [auth A] SDF format, chain MB [auth A] SDF format, chain MC [auth C] SDF format, chain NB [auth A] SDF format, chain NC [auth C] SDF format, chain OC [auth C] SDF format, chain PB [auth A] SDF format, chain PC [auth C] SDF format, chain QB [auth A] SDF format, chain QC [auth C] SDF format, chain RB [auth A] SDF format, chain RC [auth C] SDF format, chain TB [auth A] SDF format, chain UB [auth B] SDF format, chain VB [auth B] SDF format, chain WB [auth B] SDF format, chain XB [auth B] SDF format, chain YB [auth B] SDF format, chain ZB [auth B] SDF format, chain SB [auth A] SDF format, chain OB [auth A] SDF format, chain LC [auth C] MOL2 format, chain AC [auth B] MOL2 format, chain BC [auth B] MOL2 format, chain CC [auth B] MOL2 format, chain DC [auth B] MOL2 format, chain EC [auth B] MOL2 format, chain FC [auth B] MOL2 format, chain GC [auth C] MOL2 format, chain HC [auth C] MOL2 format, chain IB [auth A] MOL2 format, chain IC [auth C] MOL2 format, chain JB [auth A] MOL2 format, chain JC [auth C] MOL2 format, chain KB [auth A] MOL2 format, chain KC [auth C] MOL2 format, chain LB [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain MC [auth C] MOL2 format, chain NB [auth A] MOL2 format, chain NC [auth C] MOL2 format, chain OC [auth C] MOL2 format, chain PB [auth A] MOL2 format, chain PC [auth C] MOL2 format, chain QB [auth A] MOL2 format, chain QC [auth C] MOL2 format, chain RB [auth A] MOL2 format, chain RC [auth C] MOL2 format, chain TB [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain VB [auth B] MOL2 format, chain WB [auth B] MOL2 format, chain XB [auth B] MOL2 format, chain YB [auth B] MOL2 format, chain ZB [auth B] MOL2 format, chain SB [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain LC [auth C] mmCIF format, chain AC [auth B] mmCIF format, chain BC [auth B] mmCIF format, chain CC [auth B] mmCIF format, chain DC [auth B] mmCIF format, chain EC [auth B] mmCIF format, chain FC [auth B] mmCIF format, chain GC [auth C] mmCIF format, chain HC [auth C] mmCIF format, chain IB [auth A] mmCIF format, chain IC [auth C] mmCIF format, chain JB [auth A] mmCIF format, chain JC [auth C] mmCIF format, chain KB [auth A] mmCIF format, chain KC [auth C] mmCIF format, chain LB [auth A] mmCIF format, chain MB [auth A] mmCIF format, chain MC [auth C] mmCIF format, chain NB [auth A] mmCIF format, chain NC [auth C] mmCIF format, chain OC [auth C] mmCIF format, chain PB [auth A] mmCIF format, chain PC [auth C] mmCIF format, chain QB [auth A] mmCIF format, chain QC [auth C] mmCIF format, chain RB [auth A] mmCIF format, chain RC [auth C] mmCIF format, chain TB [auth A] mmCIF format, chain UB [auth B] mmCIF format, chain VB [auth B] mmCIF format, chain WB [auth B] mmCIF format, chain XB [auth B] mmCIF format, chain YB [auth B] mmCIF format, chain ZB [auth B] mmCIF format, chain SB [auth A] mmCIF format, chain OB [auth A] mmCIF format, chain LC [auth C]	AC [auth B] BC [auth B] CC [auth B] DC [auth B] EC [auth B] AC [auth B], BC [auth B], CC [auth B], DC [auth B], EC [auth B], FC [auth B], GC [auth C], HC [auth C], IB [auth A], IC [auth C], JB [auth A], JC [auth C], KB [auth A], KC [auth C], LB [auth A], LC [auth C], MB [auth A], MC [auth C], NB [auth A], NC [auth C], OB [auth A], OC [auth C], PB [auth A], PC [auth C], QB [auth A], QC [auth C], RB [auth A], RC [auth C], SB [auth A], TB [auth A], UB [auth B], VB [auth B], WB [auth B], XB [auth B], YB [auth B], ZB [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AC [auth B] Focus chain BC [auth B] Focus chain CC [auth B] Focus chain DC [auth B] Focus chain EC [auth B] Focus chain FC [auth B] Focus chain GC [auth C] Focus chain HC [auth C] Focus chain IB [auth A] Focus chain IC [auth C] Focus chain JB [auth A] Focus chain JC [auth C] Focus chain KB [auth A] Focus chain KC [auth C] Focus chain LB [auth A] Focus chain LC [auth C] Focus chain MB [auth A] Focus chain MC [auth C] Focus chain NB [auth A] Focus chain NC [auth C] Focus chain OB [auth A] Focus chain OC [auth C] Focus chain PB [auth A] Focus chain PC [auth C] Focus chain QB [auth A] Focus chain QC [auth C] Focus chain RB [auth A] Focus chain RC [auth C] Focus chain SB [auth A] Focus chain TB [auth A] Focus chain UB [auth B] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B] Interactions & Density Focus chain AC [auth B] Focus chain BC [auth B] Focus chain CC [auth B] Focus chain DC [auth B] Focus chain EC [auth B] Focus chain FC [auth B] Focus chain GC [auth C] Focus chain HC [auth C] Focus chain IB [auth A] Focus chain IC [auth C] Focus chain JB [auth A] Focus chain JC [auth C] Focus chain KB [auth A] Focus chain KC [auth C] Focus chain LB [auth A] Focus chain LC [auth C] Focus chain MB [auth A] Focus chain MC [auth C] Focus chain NB [auth A] Focus chain NC [auth C] Focus chain OB [auth A] Focus chain OC [auth C] Focus chain PB [auth A] Focus chain PC [auth C] Focus chain QB [auth A] Focus chain QC [auth C] Focus chain RB [auth A] Focus chain RC [auth C] Focus chain SB [auth A] Focus chain TB [auth A] Focus chain UB [auth B] Focus chain VB [auth B] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B] Focus chain ZB [auth B]