8OPM

Human Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (closed state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Sialoglycan binding triggers spike opening in a human coronavirus.

Pronker, M.F.Creutznacher, R.Drulyte, I.Hulswit, R.J.G.Li, Z.van Kuppeveld, F.J.M.Snijder, J.Lang, Y.Bosch, B.J.Boons, G.J.Frank, M.de Groot, R.J.Hurdiss, D.L.

(2023) Nature 624: 201-206

  • DOI: https://doi.org/10.1038/s41586-023-06599-z
  • Primary Citation of Related Structures:  
    8OHN, 8OPM, 8OPN, 8OPO

  • PubMed Abstract: 

    Coronavirus spike proteins mediate receptor binding and membrane fusion, making them prime targets for neutralizing antibodies. In the cases of severe acute respiratory syndrome coronavirus, severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus, spike proteins transition freely between open and closed conformations to balance host cell attachment and immune evasion 1-5 . Spike opening exposes domain S1 B , allowing it to bind to proteinaceous receptors 6,7 , and is also thought to enable protein refolding during membrane fusion 4,5 . However, with a single exception, the pre-fusion spike proteins of all other coronaviruses studied so far have been observed exclusively in the closed state. This raises the possibility of regulation, with spike proteins more commonly transitioning to open states in response to specific cues, rather than spontaneously. Here, using cryogenic electron microscopy and molecular dynamics simulations, we show that the spike protein of the common cold human coronavirus HKU1 undergoes local and long-range conformational changes after binding a sialoglycan-based primary receptor to domain S1 A . This binding triggers the transition of S1 B domains to the open state through allosteric interdomain crosstalk. Our findings provide detailed insight into coronavirus attachment, with possibilities of dual receptor usage and priming of entry as a means of immune escape.


  • Organizational Affiliation

    Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein,General control transcription factor GCN4
A, B, C
1,326Human coronavirus HKU1Saccharomyces cerevisiae
This entity is chimeric
Mutation(s): 15 
UniProt
Find proteins for E0YJ44 (Human coronavirus HKU1)
Explore E0YJ44 
Go to UniProtKB:  E0YJ44
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03069 
Go to UniProtKB:  P03069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsE0YJ44P03069
Glycosylation
Glycosylation Sites: 21Go to GlyGen: P03069-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
D,
DA [auth d],
F,
HA [auth h],
BA [auth b],
D,
DA [auth d],
F,
HA [auth h],
J,
JA [auth j],
L,
P,
R,
V,
X
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-8)-N-acetyl-alpha-neuraminic acidAA [auth a],
MA [auth m],
O
2N/A
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth B]
BB [auth B]
CB [auth B]
DB [auth B]
EB [auth B]
AB [auth B],
BB [auth B],
CB [auth B],
DB [auth B],
EB [auth B],
FB [auth B],
GB [auth B],
HB [auth C],
IB [auth C],
JB [auth C],
KB [auth C],
LB [auth C],
MB [auth C],
NA [auth A],
NB [auth C],
OA [auth A],
OB [auth C],
PA [auth A],
PB [auth C],
QA [auth A],
QB [auth C],
RA [auth A],
SA [auth A],
TA [auth A],
UA [auth A],
VA [auth A],
WA [auth A],
XA [auth B],
YA [auth B],
ZA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2-4158
MODEL REFINEMENTCoot0.9.8.1
RECONSTRUCTIONcryoSPARC4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)NetherlandsVI.Veni.202.271
Chinese Scholarship CouncilChina2014-03250042

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection
  • Version 1.2: 2023-10-04
    Changes: Database references, Refinement description
  • Version 1.3: 2023-10-18
    Changes: Database references
  • Version 1.4: 2023-12-13
    Changes: Database references
  • Version 1.5: 2024-11-20
    Changes: Data collection, Structure summary