7QB5

Coxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-linked sialic acid inhibitor

PDB DOI: https://doi.org/10.2210/pdb7QB5/pdb

Classification: VIRUS
Organism(s): Coxsackievirus A24
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-11-18 Released: 2022-05-18
Deposition Author(s): Zocher, G., Stehle, T.
Funding Organization(s): Baden-Wuerttemberg-Stiftung

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Work: 0.166

wwPDB Validation 3D Report Full Report

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

Literature

Exploring divalent conjugates of 5- N -acetyl-neuraminic acid as inhibitors of coxsackievirus A24 variant (CVA24v) transduction.

Johansson, E., Caraballo, R., Zocher, G., Mistry, N., Arnberg, N., Stehle, T., Elofsson, M.

(2022) RSC Adv 12: 2319-2331

PubMed: 35425270 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d1ra08968d
Primary Citation of Related Structures:
7QB5

PubMed Abstract:
Coxsackievirus A24 variant (CVA24v) is responsible for several outbreaks and two pandemics of the highly contagious eye infection acute hemorrhagic conjunctivitis (AHC). Currently, neither prevention (vaccines) nor treatments (antivirals) are available for combating this disease. CVA24v attaches to cells by binding Neu5Ac-containing glycans on the surface of cells which facilitates entry. Previously, we have demonstrated that pentavalent Neu5Ac conjugates attenuate CVA24v infection of human corneal epithelial (HCE) cells. In this study, we report on the structure-based design of three classes of divalent Neu5Ac conjugates, with varying spacer lengths, and their effect on CVA24v transduction in HCE cells. In relative terms, the most efficient class of divalent Neu5Ac conjugates are more efficient than the pentavalent Neu5Ac conjugates previously reported.

Organizational Affiliation

Department of Chemistry, Umeå University SE90187 Umeå Sweden mikael.elofsson@umu.se.

Macromolecule Content

Total Structure Weight: 98.88 kDa
Atom Count: 7,489
Modelled Residue Count: 836
Deposited Residue Count: 885
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A [auth 111]	305	Coxsackievirus A24	Mutation(s): 0
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24) Explore V9VEF3 Go to UniProtKB: V9VEF3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V9VEF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP2	B [auth 222]	271	Coxsackievirus A24	Mutation(s): 0
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24) Explore V9VEF3 Go to UniProtKB: V9VEF3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V9VEF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C [auth 333]	240	Coxsackievirus A24	Mutation(s): 0
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24) Explore V9VEF3 Go to UniProtKB: V9VEF3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V9VEF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D [auth 444]	69	Coxsackievirus A24	Mutation(s): 0
UniProt
Find proteins for V9VEF3 (Coxsackievirus A24) Explore V9VEF3 Go to UniProtKB: V9VEF3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V9VEF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA (Subject of Investigation/LOI) Query on SIA Download Ideal Coordinates CCD File SDF format, chain E [auth 111] MOL2 format, chain E [auth 111]	E [auth 111]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain E [auth 111]
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain F [auth 111] MOL2 format, chain F [auth 111]	F [auth 111]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain F [auth 111]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth 111] SDF format, chain H [auth 111] SDF format, chain I [auth 111] SDF format, chain M [auth 222] MOL2 format, chain G [auth 111] MOL2 format, chain H [auth 111] MOL2 format, chain I [auth 111] MOL2 format, chain M [auth 222]	G [auth 111], H [auth 111], I [auth 111], M [auth 222]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth 111] Focus chain H [auth 111] Focus chain I [auth 111] Focus chain M [auth 222]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth 111] SDF format, chain K [auth 111] SDF format, chain L [auth 111] SDF format, chain N [auth 222] MOL2 format, chain J [auth 111] MOL2 format, chain K [auth 111] MOL2 format, chain L [auth 111] MOL2 format, chain N [auth 222]	J [auth 111], K [auth 111], L [auth 111], N [auth 222]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth 111] Focus chain K [auth 111] Focus chain L [auth 111] Focus chain N [auth 222]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Work: 0.166
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 305.763	α = 90
b = 365.707	β = 90
c = 366.921	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

Zocher, G.

Stehle, T.

Funding Organization	Location	Grant Number
Baden-Wuerttemberg-Stiftung	Germany	Glycobiology

Revision History (Full details and data files)

Version 1.0: 2022-05-18
Type: Initial release
Version 1.1: 2022-11-09
Changes: Database references, Derived calculations, Refinement description
Version 1.2: 2024-01-31
Changes: Data collection, Refinement description