8ZDX | pdb_00008zdx

Crystal structure of MjHKU4r-CoV-1 RBD bound to hDPP4

PDB DOI: https://doi.org/10.2210/pdb8ZDX/pdb

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Pangolin coronavirus HKU4
Expression System: Baculovirus expression vector pFastBac1-HM
Mutation(s): No

Deposited: 2024-05-03 Released: 2024-10-30
Deposition Author(s): Yang, M., Li, Z., Xu, Y., Zhang, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.252 (Depositor), 0.252 (DCC)
R-Value Work:
0.208 (Depositor), 0.208 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for human DPP4 receptor recognition by a pangolin MERS-like coronavirus.

Yang, M., Li, Z., Chen, J., Li, Y., Xu, R., Wang, M., Xu, Y., Chen, R., Ji, W., Li, X., Wei, J., Zhou, Z., Ren, M., Ma, K., Guan, J., Mo, G., Zhou, P., Shu, B., Guo, J., Yuan, Y., Shi, Z.L., Zhang, S.

(2024) PLoS Pathog 20: e1012695-e1012695

PubMed: 39514585 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1012695
Primary Citation Related Structures:
8ZDX, 8ZE6

PubMed Abstract:
Middle East respiratory syndrome coronavirus (MERS-CoV) and the pangolin MERS-like coronavirus MjHKU4r-CoV-1 employ dipeptidyl peptidase 4 (DPP4) as an entry receptor. MjHKU4r-CoV-1 could infect transgenic mice expressing human DPP4. To understand the mechanism of MjHKU4r-CoV-1 entry into cells, we determined the crystal structures of the receptor binding domain (RBD) of MjHKU4r-CoV-1 spike protein bound to human DPP4 (hDPP4) and Malayan pangolin DPP4 (MjDPP4), respectively. The overall hDPP4-binding mode of MjHKU4r-CoV-1 RBD is similar to that of MERS-CoV RBD. MjHKU4r-CoV-1 RBD shows higher binding affinity to hDPP4 compared to the bat MERS-like coronavirus Ty-BatCoV-HKU4. Via swapping residues between MjHKU4r-CoV-1 RBD and Ty-BatCoV-HKU4 RBD, we identified critical determinants on MjHKU4r-CoV-1 that are responsible for virus usage of hDPP4. Our study suggests that MjHKU4r-CoV-1 is more adapted to the human receptor compared to the bat HKU4 coronavirus and highlights the potential of virus emergence into the human population.

Organizational Affiliation

College of Life Sciences, Nanjing Agricultural University, Nanjing, China.

Macromolecule Content

Total Structure Weight: 219.21 kDa
Atom Count: 15,436
Modeled Residue Count: 1,872
Deposited Residue Count: 1,874
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 membrane form	A, B [auth C]	729	Homo sapiens	Mutation(s): 0 Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487 Go to UniProtKB: P27487
PHAROS: P27487 GTEx: ENSG00000197635
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B [auth C]	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth D], D [auth B]	208	Pangolin coronavirus HKU4	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAL8 (Pangolin coronavirus HKU4/P251T/pangolin/2018) Explore A0ACD6BAL8 Go to UniProtKB: A0ACD6BAL8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAL8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth D] Focus chain D [auth B]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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, F	3		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE (Subject of Investigation/LOI) Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth B] SDF format, chain O [auth D] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth D] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth D] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth C] O [auth D] J [auth A], K [auth A], L [auth A], M [auth C], O [auth D], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth B]