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Article ; Online: The cryo-EM structure of African swine fever virus unravels a unique architecture comprising two icosahedral protein capsids and two lipoprotein membranes.

Andrés, German / Charro, Diego / Matamoros, Tania / Dillard, Rebecca S / Abrescia, Nicola G A

2019 Volume 295, Issue 1, Page(s) 1–12

Abstract: African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease currently present in many countries of Africa, Europe, and Asia. Despite intense research efforts, relevant gaps in the ... ...

Abstract	African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease currently present in many countries of Africa, Europe, and Asia. Despite intense research efforts, relevant gaps in the architecture of the infectious virus particle remain. Here, we used single-particle cryo-EM to analyze the three-dimensional structure of the mature ASFV particle. Our results show that the ASFV virion, with a radial diameter of ∼2,080 Å, encloses a genome-containing nucleoid surrounded by two distinct icosahedral protein capsids and two lipoprotein membranes. The outer capsid forms a hexagonal lattice (triangulation number
MeSH term(s)	African Swine Fever Virus/metabolism ; African Swine Fever Virus/ultrastructure ; Animals ; Capsid/ultrastructure ; Capsid Proteins/chemistry ; Capsid Proteins/ultrastructure ; Chlorocebus aethiops ; Cryoelectron Microscopy ; Lipids/chemistry ; Protein Multimerization ; Vero Cells ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/ultrastructure
Chemical Substances	Capsid Proteins ; Lipids ; Viral Envelope Proteins
Language	English
Publishing date	2019-10-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.AC119.011196
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Article: Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods.

Stagnoli, Soledad / Peccati, Francesca / Connell, Sean R / Martinez-Castillo, Ane / Charro, Diego / Millet, Oscar / Bruzzone, Chiara / Palazon, Asis / Ardá, Ana / Jiménez-Barbero, Jesús / Ereño-Orbea, June / Abrescia, Nicola G A / Jiménez-Osés, Gonzalo

Frontiers in microbiology

2022 Volume 13, Page(s) 870938

Abstract: Two years after its emergence, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several vaccines. The extensively glycosylated ...

Abstract	Two years after its emergence, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several vaccines. The extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin converting enzyme 2 (ACE2) through its receptor binding domain (RBD), is the major target of neutralizing antibodies. Like to many other viral fusion proteins, the SARS-CoV-2 spike protein utilizes a glycan shield to thwart the host immune response. To grasp the influence of chemical signatures on carbohydrate mobility and reconcile the cryo-EM density of specific glycans we combined our cryo-EM map of the S ectodomain to 4.1 Å resolution, reconstructed from a limited number of particles, and all-atom molecular dynamics simulations. Chemical modifications modeled on representative glycans (defucosylation, sialylation and addition of terminal LacNAc units) show no significant influence on either protein shielding or glycan flexibility. By estimating at selected sites the local correlation between the full density map and atomic model-based maps derived from molecular dynamics simulations, we provide insight into the geometries of the α-Man-(1→3)-[α-Man-(1→6)-]-β-Man-(1→4)-β-GlcNAc(1→4)-β-GlcNAc core common to all
Language	English
Publishing date	2022-04-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.870938
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Article ; Online: Structural basis for assembly of vertical single β-barrel viruses.

Santos-Pérez, Isaac / Charro, Diego / Gil-Carton, David / Azkargorta, Mikel / Elortza, Felix / Bamford, Dennis H / Oksanen, Hanna M / Abrescia, Nicola G A

Nature communications

2019 Volume 10, Issue 1, Page(s) 1184

Abstract: The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the ...

Abstract	The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs.
MeSH term(s)	Archaeal Viruses/physiology ; Capsid Proteins/chemistry ; Capsid Proteins/metabolism ; Capsid Proteins/ultrastructure ; Cryoelectron Microscopy ; DNA Viruses/physiology ; Haloarcula/virology ; Models, Molecular ; Protein Conformation, beta-Strand ; Protein Multimerization ; Virion/ultrastructure ; Virus Assembly
Chemical Substances	Capsid Proteins
Language	English
Publishing date	2019-03-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-08927-2
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Article ; Online: A novel Schmallenberg virus subunit vaccine candidate protects IFNAR

Boshra, Hani / Lorenzo, Gema / Charro, Diego / Moreno, Sandra / Guerra, Gabriel Soares / Sanchez, Isbene / Garrido, Joseba M / Geijo, Marivi / Brun, Alejandro / Abrescia, Nicola G A

Scientific reports

2020 Volume 10, Issue 1, Page(s) 18725

Abstract: Schmallenberg virus (SBV), an arthropod-transmitted pathogenic bunyavirus, continues to be a threat to the European livestock industry, causing morbidity and mortality among young ruminant livestock. Here, we describe a novel SBV subunit vaccine, based ... ...

Abstract	Schmallenberg virus (SBV), an arthropod-transmitted pathogenic bunyavirus, continues to be a threat to the European livestock industry, causing morbidity and mortality among young ruminant livestock. Here, we describe a novel SBV subunit vaccine, based on bacterially expressed SBV nucleoprotein (SBV-N) administered with a veterinary-grade Saponin adjuvant. When assayed in an IFNAR
MeSH term(s)	Adjuvants, Immunologic/administration & dosage ; Animals ; Antibodies, Viral/biosynthesis ; Antibody Specificity ; Broadly Neutralizing Antibodies/biosynthesis ; Bunyaviridae Infections/immunology ; Bunyaviridae Infections/prevention & control ; Bunyaviridae Infections/veterinary ; In Vitro Techniques ; Interferon-gamma/metabolism ; Lymphocyte Activation ; Mice ; Mice, Knockout ; Orthobunyavirus/genetics ; Orthobunyavirus/immunology ; Orthobunyavirus/pathogenicity ; Receptor, Interferon alpha-beta/deficiency ; Receptor, Interferon alpha-beta/genetics ; Ruminants ; Saponins/administration & dosage ; Vaccines, Subunit/administration & dosage ; Vaccines, Subunit/genetics ; Vaccines, Subunit/immunology ; Viral Vaccines/administration & dosage ; Viral Vaccines/genetics ; Viral Vaccines/immunology
Chemical Substances	Adjuvants, Immunologic ; Antibodies, Viral ; Broadly Neutralizing Antibodies ; Ifnar1 protein, mouse ; Saponins ; Vaccines, Subunit ; Viral Vaccines ; Receptor, Interferon alpha-beta (156986-95-7) ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2020-11-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-73424-2
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Article ; Online: DNA vaccination regimes against Schmallenberg virus infection in IFNAR

Boshra, Hani Y / Charro, Diego / Lorenzo, Gema / Sánchez, Isbene / Lazaro, Beatriz / Brun, Alejandro / Abrescia, Nicola G A

Antiviral research

2017 Volume 141, Page(s) 107–115

Abstract: Schmallenberg virus (SBV) is an RNA virus of the Bunyaviridae family, genus Orthobunyavirus that infects wild and livestock species of ruminants. While inactivated and attenuated vaccines have been shown to prevent SBV infection, little is known about ... ...

Abstract	Schmallenberg virus (SBV) is an RNA virus of the Bunyaviridae family, genus Orthobunyavirus that infects wild and livestock species of ruminants. While inactivated and attenuated vaccines have been shown to prevent SBV infection, little is known about their mode of immunity; specifically, which components of the virus are responsible for inducing immunological responses in the host. As previous DNA vaccination experiments on other bunyaviruses have found that glycoproteins, as well as modified (i.e. ubiquitinated) nucleoproteins (N) can confer immunity against virulent viral challenge, constructs encoding for fragments of SBV glycoproteins G
Language	English
Publishing date	2017-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2017.02.013
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Zs.A 1627: Show issues

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Article ; Online: Minimal epitope for Mannitou IgM on paucimannose-carrying glycoproteins.

Glycobiology

2021 Volume 31, Issue 8, Page(s) 1005–1017

Abstract: Paucimannosidic glycans are restricted to the core structure [Man1-3GlcNAc2Fuc0-1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal ... ...

Abstract	Paucimannosidic glycans are restricted to the core structure [Man1-3GlcNAc2Fuc0-1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal and liver cancer. Mannitou IgM is a murine monoclonal antibody that was previously shown to recognize Man3GlcNAc2 with an almost exclusive selectivity. Here, we have sought the definition of the minimal glycan epitope of Mannitou IgM, initiated by screening on a newly designed paucimannosidic glycan microarray; among the best binders were Man3GlcNAc2 and its α1,6 core-fucosylated variant, Man3GlcNAc2Fuc1. Unexpectedly and in contrast to earlier findings, Man5GlcNAc2-type structures bind equally well and a large tolerance was observed for substitutions on the α1,6 arm. It was confirmed that any substitution on the single α1,3-linked mannose completely abolishes binding. Surface plasmon resonance for kinetic measurements of Mannitou IgM binding, either directly on the glycans or as presented on omega-1 and kappa-5 soluble egg antigens from the helminth parasite Schistosoma mansoni, showed submicromolar affinities. To characterize the epitope in greater and atomic detail, saturation transfer difference nuclear magnetic resonance spectroscopy was performed with the Mannitou antigen-binding fragment. The STD-NMR data demonstrated the strongest interactions with the aliphatic protons H1 and H2 of the α1-3-linked mannose and weaker imprints on its H3, H4 and H5 protons. In conclusion, Mannitou IgM binding requires a nonsubstituted α1,3-linked mannose branch of paucimannose also on proteins, making it a highly specific tool for the distinction of concurrent human tumor-associated carbohydrate antigens.
MeSH term(s)	Animals ; DNA-Binding Proteins ; Epitopes/chemistry ; Fucose/metabolism ; Glycoproteins/metabolism ; Humans ; Immunoglobulin M ; Mammals/metabolism ; Membrane Proteins ; Mice ; Polysaccharides/chemistry ; Schistosoma mansoni/chemistry ; Schistosoma mansoni/metabolism
Chemical Substances	DNA-Binding Proteins ; Epitopes ; Glycoproteins ; Immunoglobulin M ; Man1 protein, mouse ; Membrane Proteins ; Polysaccharides ; Fucose (28RYY2IV3F)
Language	English
Publishing date	2021-04-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
DOI	10.1093/glycob/cwab027
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Article ; Online: Minimal epitope for Mannitou IgM on paucimannose-carrying glycoproteins

Glycobiology

2021 Volume 31, Issue 8

Abstract: Paucimannosidic glycans are restricted to the core structure [Man1–3GlcNAc2Fuc0–1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal ... ...

Abstract	Paucimannosidic glycans are restricted to the core structure [Man1–3GlcNAc2Fuc0–1] of N-glycans and are rarely found in mammalian tissues. Yet, especially [Man2-3GlcNAc2Fuc1] have been found significantly upregulated in tumors, including in colorectal and liver cancer. Mannitou IgM is a murine monoclonal antibody that was previously shown to recognise Man3GlcNAc2 with an almost exclusive selectivity. Here, we have sought the definition of the minimal glycan epitope of Mannitou IgM, initiated by screening on a newly designed paucimannosidic glycan microarray. Among the best binders were Man3GlcNAc2 and its α1,6 core-fucosylated variant, Man3GlcNAc2Fuc1. Unexpectedly and in contrast to earlier findings, Man5GlcNAc2-type structures bind equally well and a large tolerance was observed for substitutions on the α1,6 arm. It was confirmed that any substitution on the single α1,3-linked mannose completely abolishes binding. Surface plasmon resonance for kinetic measurements of Mannitou IgM binding, either directly on the glycans or as presented on omega-1 and kappa-5 soluble egg antigens from the helminth parasite Schistosoma mansoni, showed submicromolar affinities. To characterize the epitope in greater and atomic detail, saturation transfer difference nuclear magnetic resonance spectroscopy was performed with the Mannitou antigen-binding fragment. The STD-NMR data demonstrated the strongest interactions with the aliphatic protons H1 and H2 of the α1–3-linked mannose, and weaker imprints on its H3, H4 and H5 protons. In conclusion, Mannitou IgM binding requires a non-substituted α1,3-linked mannose branch of paucimannose also on proteins, making it a highly specific tool for the distinction of concurrent human tumor-associated carbohydrate antigens.
Keywords	IgM ; Mannitou ; N-glycan ; core fucose ; paucimannosidic epitopes
Subject code	570
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Insight into the Assembly of Viruses with Vertical Single β-barrel Major Capsid Proteins.

Gil-Carton, David / Jaakkola, Salla T / Charro, Diego / Peralta, Bibiana / Castaño-Díez, Daniel / Oksanen, Hanna M / Bamford, Dennis H / Abrescia, Nicola G A

Structure (London, England : 1993)

2015 Volume 23, Issue 10, Page(s) 1866–1877

Abstract: Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of life. Here, using biochemical and cryo-electron ... ...

Abstract	Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of life. Here, using biochemical and cryo-electron microscopy techniques, we solved the structure of euryarchaeal, halophilic, internal membrane-containing Haloarcula hispanica icosahedral virus 2 (HHIV-2). We show that the density of the two major capsid proteins (MCPs) recapitulates vertical single β-barrel proteins and that disulfide bridges stabilize the capsid. Below, ordered density is visible close to the membrane and at the five-fold vertices underneath the host-interacting vertex complex underpinning membrane-protein interactions. The HHIV-2 structure exemplifies the division of conserved architectural elements of a virion, such as the capsid, from those that evolve rapidly due to selective environmental pressure such as host-recognizing structures. We propose that in viruses with two vertical single β-barrel MCPs the vesicle is indispensable, and membrane-protein interactions serve as protein-railings for guiding the assembly.
MeSH term(s)	Archaeal Viruses/genetics ; Archaeal Viruses/metabolism ; Archaeal Viruses/ultrastructure ; Binding Sites ; Capsid/metabolism ; Capsid/ultrastructure ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Disulfides ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genome, Viral ; Haloarcula/virology ; Models, Molecular ; Protein Binding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Salt-Tolerance ; Virion/genetics ; Virion/metabolism ; Virion/ultrastructure ; Virus Assembly
Chemical Substances	Capsid Proteins ; Disulfides ; Recombinant Proteins
Language	English
Publishing date	2015-10-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2015.07.015
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