View source for 9tkm


==CryoEM structure of coxsackievirus B1 virus-like particle with VP4 deletion==
<StructureSection load='9tkm' size='340' side='right'caption='[[9tkm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9tkm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_B1 Coxsackievirus B1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9TKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9TKM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9tkm OCA], [https://pdbe.org/9tkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9tkm RCSB], [https://www.ebi.ac.uk/pdbsum/9tkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9tkm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/POLG_CXB1J POLG_CXB1J] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity). Capsid protein VP1 mainly forms the vertices of the capsid (By similarity). Capsid protein VP1 interacts with host cell receptor to provide virion attachment to target host cells (By similarity). This attachment induces virion internalization (By similarity). Tyrosine kinases are probably involved in the entry process (By similarity). After binding to its receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized (By similarity). Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm (By similarity).[UniProtKB:P03300]  Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity).[UniProtKB:P03300]  Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (By similarity).[UniProtKB:P03300]  Lies on the inner surface of the capsid shell (By similarity). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm (By similarity).[UniProtKB:P03300]  Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation (By similarity). Allows the capsid to remain inactive before the maturation step (By similarity).[UniProtKB:P03300]  Cysteine protease that cleaves viral polyprotein and specific host proteins (By similarity). It is responsible for the autocatalytic cleavage between the P1 and P2 regions, which is the first cleavage occurring in the polyprotein (By similarity). Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation (By similarity). Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores (By similarity). Counteracts stress granule formation probably by antagonizing its assembly or promoting its dissassembly (By similarity). Cleaves and inhibits host IFIH1/MDA5, thereby inhibiting the type-I IFN production and the establishment of the antiviral state (By similarity). Cleaves and inhibits host MAVS, thereby inhibiting the type-I IFN production and the establishment of the antiviral state (By similarity).[UniProtKB:P03300][UniProtKB:P03313]  Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication.[UniProtKB:P03300]  Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3.[UniProtKB:P03300]  Localizes the viral replication complex to the surface of membranous vesicles. Together with protein 3CD binds the Cis-Active RNA Element (CRE) which is involved in RNA synthesis initiation. Acts as a cofactor to stimulate the activity of 3D polymerase, maybe through a nucleid acid chaperone activity.[UniProtKB:P03300]  Localizes the viral replication complex to the surface of membranous vesicles (By similarity). It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the disassembly of the Golgi complex, possibly through GBF1 interaction (By similarity). This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface (By similarity). Plays an essential role in viral RNA replication by recruiting ACBD3 and PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (By similarity).[UniProtKB:P03300][UniProtKB:P03313]  Acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU (By similarity). The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome (By similarity). Following genome release from the infecting virion in the cytoplasm, the VPg-RNA linkage is probably removed by host TDP2 (By similarity). During the late stage of the replication cycle, host TDP2 is excluded from sites of viral RNA synthesis and encapsidation, allowing for the generation of progeny virions (By similarity).[UniProtKB:P03300]  Involved in the viral replication complex and viral polypeptide maturation. It exhibits protease activity with a specificity and catalytic efficiency that is different from protease 3C. Protein 3CD lacks polymerase activity. Protein 3CD binds to the 5'UTR of the viral genome.[UniProtKB:P03300]  Replicates the viral genomic RNA on the surface of intracellular membranes. May form linear arrays of subunits that propagate along a strong head-to-tail interaction called interface-I. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss(+)RNA genomes are either translated, replicated or encapsidated.[UniProtKB:P03300]  Major viral protease that mediates proteolytic processing of the polyprotein (By similarity). Cleaves host EIF5B, contributing to host translation shutoff (By similarity). Cleaves also host PABPC1, contributing to host translation shutoff (By similarity). Cleaves host NLRP1, triggers host N-glycine-mediated degradation of the autoinhibitory NLRP1 N-terminal fragment (By similarity).[UniProtKB:P03300][UniProtKB:P03303]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Enteroviruses, including coxsackievirus B1 (CVB1), cause severe diseases such as myocarditis and meningitis, but vaccines are lacking for most enteroviruses. Conserved and immunodominant epitopes, such as VP4 region and VP1 N-terminus may limit vaccine efficacy by inducing non-neutralizing antibody responses. Virus-like particles (VLPs) mimic native viruses without genetic material and can be engineered to exclude epitopes. To address these challenges, we developed a CVB1-VLP lacking VP4. METHODS: Sequence conservation of CVB VP4 protein and the VP1 N-terminal PALXA region was assessed, and BALB/c mice were sequentially immunized with different formalin inactivated CVB vaccines. VLPDeltaVP4 was produced using baculovirus-insect cell expression system, was purified, and characterized by SDS-PAGE, transmission electron microscopy, dynamic light scattering, cryogenic electron microscopy, three-dimensional image reconstruction and atomic modelling. VLPDeltaVP4 stability was monitored over five years at 8 degrees C. Comprehensive preclinical experiments were conducted in mice with VLPDeltaVP4, VLPDeltapalxa and inactivated CVB1. Vaccine immunogenicity was evaluated by neutralization assay, ELISA, ELISpot, and in vitro infection assays. RESULTS: VP4- and PALXA-regions were conserved among CVB serotypes and sequential mouse vaccinations confirmed the induction of antibodies against these regions, that should be avoided in vaccination. VLPDeltaVP4 exhibited &gt; 95% purity, expected morphology (~ 30 nm), exceptional stability at 8 degrees C for five years, and the atomic modelling to 2.7 A resolution showed that the particles were entirely in expanded form. Excluding VP4 from VLP improved production yield 3.5-fold, enhancing scalability of production. Immunological assays demonstrated that VLPDeltaVP4 induced slightly Th2-skewed response, but including adjuvant system 04 (AS04) in the vaccine induced balanced humoral and cellular immune response in mice. Sera from all vaccine groups modulated CVB1 infection, but IFN-alpha induction was lowest in VLP groups, suggesting reduced risk for antibody dependent enhancement of infection. VLPDeltaVP4 elicited significantly higher IFN-gamma responses compared to other vaccines, indicating robust cellular immune response. Antibody responses were comparable across adjuvanted groups, but inclusion of VP4 in the vaccine correlated with weaker systemic T-cell responses. CONCLUSIONS: VLPDeltaVP4 represents a promising next-generation CVB vaccine candidate with broad applicability against enteroviruses. Removal of VP4 may mitigate the risk for non-beneficial immune imprinting while enabling high purity, long-term stability, and improved manufacturing efficiency.

Coxsackie B1 virus-like particle that lacks VP4 protein demonstrates improved vaccine scalability, stability and immunogenicity.,Soppela S, Kyrolainen HM, Levanova A, Nekoua MP, Gonzalez-Rodriguez M, Lehto H, Ahmad KLL, Guryanov S, Hytonen VP, Laitinen OH, Junttila IS, Hober D, Butcher SJ, Hankaniemi MM J Biomed Sci. 2026 Mar 26;33(1):34. doi: 10.1186/s12929-026-01229-y. PMID:41888844<ref>PMID:41888844</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9tkm" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Coxsackievirus B1]]
[[Category: Large Structures]]
[[Category: Ahmad KLL]]
[[Category: Butcher SJ]]
[[Category: Guryanov S]]
[[Category: Levanova AL]]