8Y1D | pdb_00008y1d

2up-TM conformation of HKU1-B S protein after incubation of the receptor

PDB DOI: https://doi.org/10.2210/pdb8Y1D/pdb
EM Map EMD-38832: EMDB EMDataResource

Classification: VIRAL PROTEIN/HYDROLASE
Organism(s): Human coronavirus HKU1 (isolate N2), Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-01-24 Released: 2024-05-01
Deposition Author(s): Xia, L.Y., Zhang, Y.Y., Zhou, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for the recognition of HCoV-HKU1 by human TMPRSS2.

Xia, L., Zhang, Y., Zhou, Q.

(2024) Cell Res 34: 526-529

PubMed: 38641728 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-024-00958-9
Primary Citation Related Structures:
8Y19, 8Y1A, 8Y1B, 8Y1C, 8Y1D, 8Y1E, 8Y1F, 8Y1G, 8Y1H

Organizational Affiliation

Center for Infectious Disease Research, Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University. Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.

Macromolecule Content

Total Structure Weight: 534.76 kDa
Atom Count: 34,921
Modeled Residue Count: 4,314
Deposited Residue Count: 4,638
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,290	Human coronavirus HKU1 (isolate N2)	Mutation(s): 0 Gene Names: S, 3
UniProt
Find proteins for Q14EB0 (Human coronavirus HKU1 (isolate N2)) Explore Q14EB0 Go to UniProtKB: Q14EB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14EB0
Glycosylation
Glycosylation Sites: 22	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	D, E	384	Homo sapiens	Mutation(s): 0 Gene Names: TMPRSS2, PRSS10 EC: 3.4.21.122
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393 Go to UniProtKB: O15393
PHAROS: O15393 GTEx: ENSG00000184012
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15393
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, K, P	6		N-Glycosylation	Interactions Focus chain F Focus chain K Focus chain P Interactions & Density Focus chain F Focus chain K Focus chain P
Glycosylation Resources
GlyTouCan: G98400NB GlyCosmos: G98400NB GlyGen: G98400NB

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, L G, H, I, J, L, M, N, O, Q, R, S, T	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain EA [auth A] SDF format, chain EB [auth C] SDF format, chain FA [auth A] SDF format, chain FB [auth C] SDF format, chain GA [auth A] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain JA [auth A] SDF format, chain JB [auth C] SDF format, chain KA [auth A] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain QB [auth C] SDF format, chain RA [auth B] SDF format, chain RB [auth C] SDF format, chain SB [auth C] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain U [auth A] SDF format, chain SA [auth B] SDF format, chain QA [auth B] SDF format, chain OB [auth C] SDF format, chain NB [auth C] SDF format, chain IA [auth A] SDF format, chain HA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain SB [auth C] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain HA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain QB [auth C] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth C] mmCIF format, chain SB [auth C] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain NB [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain HA [auth A]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], IB [auth C], JA [auth A], JB [auth C], KA [auth A], KB [auth C], LA [auth B], LB [auth C], MA [auth B], MB [auth C], NA [auth B], NB [auth C], OA [auth B], OB [auth C], PA [auth B], PB [auth C], QA [auth B], QB [auth C], RA [auth B], RB [auth C], SA [auth B], SB [auth C], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]