nucleocapsid structure

Hantaan virus nucleocapsid cryo-EM structure determined at 3.3 Å resolution reveals how nucleoproteins assemble into a metastable helix containing a continuous RNA-binding groove compatible with genome encapsidation and compaction. Structure of the respiratory syncytial virus polymerase complex. ; Crepin, T.; Kolakofsky, D. Nucleoproteins and nucleocapsids of negative-strand RNA viruses. Although the overall structure is similar as other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Nucleocapsid assembly in pneumoviruses is regulated by conformational switching of the N protein. ; Cusack, S.; Rambo, R.P. 1. Crystal structure of a nucleocapsid-like nucleoprotein-RNA complex of respiratory syncytial virus. Hodges, J.; Tang, X.; Landesman, M.B. The L polymerase subunit cannot recognize the nucleocapsid alone. This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Chenavas, S.; Estrozi, L.F.; Slama-Schwok, A.; Delmas, B.; Di Primo, C.; Baudin, F.; Li, X.; Crépin, T.; Ruigrok, R.W. Wichgers Schreur, P.J. Reguera, J.; Malet, H.; Weber, F.; Cusack, S. Structural basis for encapsidation of genomic RNA by La Crosse, Niu, F.; Shaw, N.; Wang, Y.E. Ogino, M.; Gupta, N.; Green, T.J.; Ogino, T. A dual-functional priming-capping loop of rhabdoviral RNA polymerases directs terminal de novo initiation and capping intermediate formation. The core region adopts a five-stranded U-shaped right-handed antiparallel β . The nucleocapsid is the active template for transcription and replication (2, 3). Insight into how P delivers the polymerase complex to the nucleocapsid has long been pursued by reverse genetics and biochemical approaches. Application of cryo-electron tomography and subtomogram averaging to determine the structure of the Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. Lefkowitz, E.J. ; Fodor, E. Influenza virus RNA polymerase: Insights into the mechanisms of viral RNA synthesis. Interestingly, Tyr-256 and Asn-257 of P are unique, because each interacts with both molecules of N. The total surface area buried by the interactions between the PCTD and the 2 adjacent N molecules is 956 Å2, whereas the total surface area of the PCTD is 5,100 Å2. The authors declare no conflict of interest. COVID-19, caused by SARS-CoV-2, has resulted in severe and unprecedented economic and social disruptions in the world. Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Crystal structure of the core region of hantavirus nucleocapsid protein reveals the mechanism for ribonucleoprotein complex formation. ; Bào, Y.; Basler, C.F. Rigid body refinement of the individual domains and extensions was carried out with REFMAC5 (39). However, a concrete model of the direct interaction of N and P was still elusive. These differences were also observed in NLP structures in the absence of PCTD (4, 6). made figures and reviewed the text. The illustrations found in this and the subsequent figures were generated with PyMOL (41). Negative strand RNA viruses (NSVs) include many important human pathogens, such as influenza virus, Ebola virus, and rabies virus. Severin, C.; Terrell, J.R.; Zengel, J.R.; Cox, R.; Plemper, R.K.; He, B.; Luo, M. Releasing the genomic RNA sequestered in the mumps virus nucleocapsid. Superposition of the N290 structure with the PCTD-bound structure determined here revealed that the C loop is shifted, with many of the side chains rearranged to accommodate binding of the PCTD (Fig. This text focuses on viruses that infect humans, domestic animals and vertebrates and is based on extensive course notes from James Strauss’ virology class at the California Institute of Technology taught for over 30 years. SARS-CoV-2 N protein is a 419 amino acid long protein and is 89% identical to SARS-CoV-1 nucleocapsid. Structural insights into RNA encapsidation and helical assembly of the Toscana virus nucleoprotein. Nucleotide sequence conservation in paramyxoviruses; the concept of codon constellation. Likewise, the nature of the tripartite complex between N, P, and L is not well understood. PRRSV is the causative agent of both severe and persistent respiratory disease and reproductive failure in pigs worldwide. The N290/Se-PCTD structure was solved by molecular replacement with the previously determined N290 model (PDB ID code: 2qvj). N290/Se-PCTD crystals were grown by the hanging drop vapor diffusion method in 24-well VDX plates (Hampton Research) at 22 °C (32). ; Haupt, M.; Ruigrok, R.W. "Virion" refers to the entire virus. ; Ruigrok, R.W. 6 Nucleocapsid Structure and Function 123. ; Gerrard, S.R. As described above, L and P form the RNA polymerase that associates with the N-enwrapped template. The HCV RNA is single-stranded, positive-sense RNA that is approximately 9,600 nucleotide bases in length. The C-terminal lobe from members in, In addition to NSVs, the structure of nucleocapsid proteins from members in, The structure of VSV nucleocapsid was first solved as a nucleocapsid-like particle (NLP) [, First, the subunits of the nucleocapsid protein are parallelly aligned along the linear RNA genome. This requires that monomeric N subunits are delivered at the replication site to encapsidate the genomic RNA as it emerges from the polymerase. The models are rotated 180° with respect to Fig. Assembly of the Ebola Virus nucleoprotein from a chaperoned VP35 complex. Pflug, A.; Lukarska, M.; Resa-Infante, P.; Reich, S.; Cusack, S. Structural insights into RNA synthesis by the influenza virus transcription-replication machine. The structure of the middle multimerization domain of P (residues 107–177) was reported previously as a dimer (15). Comparison with the unbound NLP structure shows that N is largely unchanged upon binding P, with the most significant variation occurring in the C loops that bind to PCTD (Fig. Monomeric nucleoprotein of influenza A virus. ; Nichol, S.T. Use of the APS was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract W-31-109-Eng-38. progress in the field that systematically reviews the most exciting advances in scientific literature. Qanungo, K.R. The nucleocapsid (N) protein is an important antigen for coronavirus, which participate in RNA package and virus particle release. Raymond, D.D. They are spherical to pleomorphic particles, measuring between 80 and 160 nm in length. These basic residues are bonded to 2 acidic residues, Asp-358 and Glu-377, which are found on different molecules of the N protein-binding site. The nucleocapsid of many RNA viruses self-assembles very differently, forming a cylindrical structure in which the protein structural units are spatially arranged as a helix, hence the term helical symmetry.The occurrence of identical protein-protein interfaces on the structural units promotes the symmetrical assembly of the helix. The disordered N TAIL (aa 401-525) and PNT (aa 1 . The highest substitution occurs in alternating rather than adjacent N-binding positions. PubMed. Alayyoubi, M.; Leser, G.P. The two end-cap structures are electron-dense, the ring-like structures are electron-lucent, and the tail-like structure is a helical spring. This explains how the P delivers the viral polymerase specifically to the nucleocapsid for RNA synthesis. Interestingly, in the absence of PCTD, the extended loops were disordered in 3 of the 5 N monomers in the previously determined N RNA structure. 2007;368(4):1075-86. pmid:17379242 . It is composed of two separate domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), both capable of binding RNA in vitro, but each domain uses different mechanisms to bind RNA. It is composed of two separate domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), both capable of binding RNA in vitro, but each domain uses different mechanisms to bind RNA. ; Damier-Piolle, L.; Castagné, N.; MacLellan, K.; Bedouelle, H.; Bricogne, G.; Bhella, D.; et al. ; Bào, Y.; Basler, C.F. In the PCTD-bound structure presented here, all 5 of the loops were observed in the electron density maps and were easily traced. One of the unique characteristics that NSVs share is the assembly of the nucleocapsid and its role in viral RNA synthesis. Ge P, Tsao J, Schein S, Green TJ, Luo M, and Zhou ZH. The causative agent of severe acute respiratory syndrome (SARS) is the SARS-associated coronavirus, SARS-CoV. Author to whom correspondence should be addressed. . It is possible that the induced conformational changes in N and P allow the two to be associated more tightly when P binds to the nucleocapsid. ; Abelson, D.M. ; Jia, H.; Cressey, T.; Ludeke, B.; Noton, S.; et al. This tripartite complex was distinct from the transcriptase, a complex that does not contain the N protein. Subunits of the nucleocapsid protein are parallelly aligned along the RNA genome that is sandwiched between two domains composed of conserved helix motifs. PLoS Pathog. Structure unifies the viral universe. ; Smith, J.L. By contrast, the rmsd between the best representative conformer in the ensemble PCTD structure (as defined in ref. Amarasinghe, G.K.; Ayllón, M.A. published in the various research areas of the journal. Attribution. This mutated N has lost the ability to bind RNA. The nucleotides situated between subunits may possess a more flexible conformation. wrote the text. We solved the crystal structure of the CCHFV strain Baghdad-12 nucleocapsid protein (N), a potential therapeutic target, at a resolution of 2.1 Å. N comprises a large globular domain . How this occurs is unknown at this point. The present invention relates to a kind of new type structure of hud silica gel chromatographic column filling material being suitable to supper-fast separation and preparation thereof and application.The silica gel microball of present invention synthesis has clear nucleocapsid structure, and its core is atresia silica gel, and shell exists mesoporous.The first step uses temperature . All retroviruses selectively package two copies of their full-length, unspliced RNA genomes, both of which serve as templates for strand-transfer mediated recombination during reverse transcription. Arragain, B.; Reguera, J.; Desfosses, A.; Gutsche, I.; Schoehn, G.; Malet, H. High resolution cryo-EM structure of the helical RNA-bound Hantaan virus nucleocapsid reveals its assembly mechanisms. negative strand RNA virus; nucleocapsid; viral RNA-dependent RNA polymerase; cofactor; cross subunit interactions; capsid protein motif; 5H+3H, Fields’ Virilogy: Principles of Virus Structure. 288 Structural implications of the R203K/G204R mutations for RNP assembly 289 To investigate the impact of R203K/G204R on the tertiary structure of the nucleocapsid, 290 we built a structural model of the N protein based on documented cryo-EM . S.A.M. Each of these elements is involved in N-binding. ; Orton, R.J.; Siddell, S.G.; Smith, D.B. Nucleocapsid Protein Function. Comparative sedimentation coefficients of RNA extracted from plaque-forming and defective particles of vesicular stomatitis virus, Dissociation and reconstitution of the transcriptase and template activities of vesicular stomatitis B and T virions, Function and structure of RNA polymerase from vesicular stomatitis virus, Structure of the vesicular stomatitis virus nucleoprotein-RNA complex, Crystal structure of the rabies virus nucleoprotein-RNA complex, Role of intermolecular interactions of vesicular stomatitis virus nucleoprotein in RNA encapsidation, Localization and immunological characterization of antigenic domains of the rabies virus internal N and NS proteins, Structural difference recognized by a monoclonal antibody #404–11 between the rabies virus nucleocapsid (NC) produced in virus infected cells and the NC-like structures produced in the nucleoprotein (N) cDNA-transfected cells, Phosphorylation by cellular casein kinase II is essential for transcriptional activity of vesicular stomatitis virus phosphoprotein P, Role of cellular casein kinase II in the function of the phosphoprotein (P) subunit of RNA polymerase of vesicular stomatitis virus, Multimerization and transcriptional activation of the phosphoprotein (P) of vesicular stomatitis virus by casein kinase-II, Phosphorylation of specific serine residues within the acidic domain of the phosphoprotein of vesicular stomatitis virus regulates transcription in vitro, Phosphorylated states of vesicular stomatitis virus P protein in vitro and in vivo, Phosphorylation within the amino-terminal acidic domain I of the phosphoprotein of vesicular stomatitis virus is required for transcription but not for replication, Crystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus, Role of the hypervariable hinge region of phosphoprotein P of vesicular stomatitis virus in viral RNA synthesis and assembly of infectious virus particles, Cooperative binding of multimeric phosphoprotein (P) of vesicular stomatitis virus to polymerase (L) and template: Pathways of assembly, Study of the assembly of vesicular stomatitis virus N protein: Role of the P protein, Identification of a domain within the phosphoprotein of vesicular stomatitis virus that is essential for transcription in vitro, Mapping of interacting domains between the nucleocapsid protein and the phosphoprotein of vesicular stomatitis virus by using a two-hybrid system, Location of the binding domains for the RNA polymerase L and the ribonucleocapsid template within different halves of the NS phosphoprotein of vesicular stomatitis virus, Basic amino acid residues at the carboxy-terminal eleven amino acid region of the phosphoprotein (P) are required for transcription but not for replication of vesicular stomatitis virus genome RNA, The functional domains of the phosphoprotein (NS) of vesicular stomatitis virus (Indiana serotype), Solution structure of the C-terminal nucleoprotein-RNA binding domain of the vesicular stomatitis virus phosphoprotein, Complex formation with vesicular stomatitis virus phosphoprotein NS prevents binding of nucleocapsid protein N to nonspecific RNA, Kinetic, quantitative, and functional analysis of multiple forms of the vesicular stomatitis virus nucleocapsid protein in infected cells, Viral proteins required for the in vitro replication of vesicular stomatitis virus defective interfering particle genome RNA, Both NS and L proteins are required for in vitro RNA synthesis by vesicular stomatitis virus, Identification of a novel tripartite complex involved in replication of vesicular stomatitis virus genome RNA, Crystallography & NMR system: A new software suite for macromolecular structure determination, Mapping and functional role of the self-association domain of vesicular stomatitis virus phosphoprotein, Preparation and Analysis of Protein Crystals, Processsing of x-ray diffraction data collected in oscillation mode, On the treatment of negative intensity observations, COMO: A program for combined molecular replacement, Coot: Model-building tools for molecular graphics, Improved methods for building protein models in electron density maps and the location of errors in these models, Mass and molecular composition of vesicular stomatitis virus: A scanning transmission electron microscopy analysis, Refinement of macromolecular structures by the maximum-likelihood method, Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Inference of macromolecular assemblies from crystalline state, Proceedings of the National Academy of Sciences, Resuspended dust and lead pollution in London, Painted lady butterfly population fluctuations, Core Concept: In the wake of COVID-19, decentralized clinical trials get popular, Opinion: Toward inclusive global governance of human genome editing. Paramyxovirus mRNA editing, the “rule of six” and error catastrophe: A hypothesis. For members in, The encapsidation of genomic RNA in the nucleocapsid occurs concomitantly with viral RNA replication. This book serves as a useful volume for basic scientists, graduate students, and practicing clinicians in understanding the pathobiology, etiology, and treatment of this disease. In paramyxoviruses such as Sendai virus, there is so called “rule of six” that stipulates that the viral genome is only replicated efficiently when the genome length is 6n nucleotides (n is an integral number) [, Other features also suggest that the nucleocapsid protein plays a role in viral RNA synthesis. Renner, M.; Bertinelli, M.; Leyrat, C.; Paesen, G.C. This Concept Map, created with IHMC CmapTools, has information related to: Answers_Viral structure, may have an envelope origin derived from host cell membranes by a process called budding, enveloped viruses composition surrounds either a polyhedral or helical nucleocapsid, unmethylated cytosine-guanine dinucleotide sequences; double- stranded viral RNA; single-stranded viral RNA bind to PRRs . (A) CryoEM structure of the nucleocapsid complex, determined at 3.6 Å resolution. Each N monomer accommodates 9 bases of RNA. Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA. Proceedings of the VIIth International Symposium held in Segovia, Spain, May 10-15, 1997 ; Sachse, C.; Schoehn, G. Structural virology: Near-atomic cryo-EM structure of the helical measles virus nucleocapsid. Crude placement of the PCTD domains was performed with the aid of an intermediate VSV N/RNA–PCTD model using the superpositioning protocols in O (37). One of the unique characteristics that NSVs share is the assembly of the nucleocapsid and its role in viral RNA synthesis. Chen CY, Chang CK, Chang YW, Sue SC, Bai HI, Riang L, et al. This is proved by the fact that a similar capsid could be assembled in the absence of RNA [, This assembly scheme of linear nucleocapsid is maintained in all members in the order, The assembly of the nucleocapsid takes place while the new genomic RNA is replicated for both the viral RNA (- sense) and complimentary RNA (+ sense) genomes. Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV). The P dimer maintains the association of the viral polymerase with the nucleocapsid throughout the process of RNA synthesis. Ge, P.; Tsao, J.; Schein, S.; Green, T.J.; Luo, M.; Zhou, Z.H. Here, N comes into contact with the newly synthesized genomic RNA, and the process of encapsidation occurs. 2015. Structural basis for RNA binding and homo-oligomer formation by influenza B virus nucleoprotein. Cox, R.; Pickar, A.; Qiu, S.; Tsao, J.; Rodenburg, C.; Dokland, T.; Elson, A.; He, B.; Luo, M. Structural studies on the authentic mumps virus nucleocapsid showing uncoiling by the phosphoprotein. and M.L. The Paramyxoviruses infect many species including mammals, birds, reptiles, and fish and pose a significant health and economic burden worldwide. The N290–Se-PCTD protein complex was mixed with a 1:1 volume equivalent of reservoir solution consisting of 0.8–1.0 M K/Na tartrate, 200 mM NaCl, and 100 mM imidazole buffer, pH 8.0. 2). wwPDB Validation   3D Report Full Report, (2020) Acta Pharm Sin B 10: 1228-1238. The 5 monomers overlaid as a single rigid body had an rmsd of 1.117 Å. ; et al. Negative strand RNA viruses (NSVs) include many important human pathogens, such as influenza virus, Ebola virus, and rabies virus. The N protein is present in the nucleocapsid as a linear polymer. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA. It was also reported recently that the structure of the uncomplexed C-terminal 71 aa of P (residues 195–265) contains a single compact domain comprising an antiparallel β-turn and 5 α-helices (24). Anhlan, D.; Grundmann, N.; Makalowski, W.; Ludwig, S.; Scholtissek, C. Origin of the 1918 pandemic H1N1 influenza A virus as studied by codon usage patterns and phylogenetic analysis. The L protein or the L–P complex could cause this local dissociation, exposing the RNA in the course of polynucleotide synthesis. PNAS is a partner of CHORUS, COPE, CrossRef, ORCID, and Research4Life. Interestingly, the integrity of the assembled nucleocapsid is not completely broken. Crystal structure of the SARS coronavirus nucleocapsid protein dimerization domain I-Mei Yu 1,3, Michael L. Oldham1,3, Jingqiang Zhang2, and Jue Chen1,* 1Department of Biological Sciences and the Cancer Center, Purdue University, West Lafayette, IN 47907 2State Key Lab for Biocontrol, Zhongshan University, Guangzhou, P.R.China 3These authors contributed equally to this work The P dimer in the viral polymerase delivers the L subunit to the nucleocapsid template. Define nucleocapsid. ; Luo, M. Structure of the vesicular stomatitis virus nucleoprotein-RNA complex. In our model a single C-terminal domain of P is required for recognition of the nucleocapsid. The perspective represented by this book, that of medical virology as an infectious disease science, is meant to provide a starting point, an anchor, for those who must relate the subject to clinical practice, public health practice, ... ; Tao, Y.J. 3. Cristina, J.; Moreno, P.; Moratorio, G.; Musto, H. Genome-wide analysis of codon usage bias in Ebolavirus. ; Kormelink, R.; Kortekaas, J. Genome packaging of the Bunyavirales. 2015. The assembly of nucleocapsid is the crucial step in the process of the formation of infectious virion; therefore, revealing the mechanism of EBV nucleocapsid assembly should inform the rational . Likewise, topologically, P is unchanged upon binding to the nucleocapsid. Recently, more insight into capsid formation was gained through crystallographic studies of an N protein with a serine-to-tryptophan mutation at residue 290 (called N290; ref. Pagan, I.; Holmes, E.C. As amounts of this encapsidation precursor complex increase, the switch to replication is initiated. Viruses are composed of two fundamental units, . This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. The capsid gives shape and symmetry to the viral particle and protects its genome. VSV has long served as a prototypic nonsegmented negative-strand RNA virus (NNSRV), partly because of the small number of genes that are encoded by its 11-kb genome (1). Neither serine makes contact with the N protein but, rather, each sits exposed ≈50 Å directly above the entrance of the RNA encapsidation cavity and aligned with the interior face of the C lobe of the N protein. Gumpper, R.H.; Li, W.; Luo, M. Contrains of viral RNA synthesis on codon usage of negative strand RNA virus. 1. ; Gay, L.S. Before data collection, crystals were cryoprotected stepwise to a final solution containing reservoir solution plus 20% glycerol and were flash frozen in liquid nitrogen. This book provides essential information on these viruses and the development of vaccines to control coronavirus infections. Coronaviruses are the RNA viruses with the largest genome known to date (27 to 32 kb). SARS was the ?rst new plague of the twenty-?rst century. Within months, it spread worldwide from its “birthplace” in Guangdong Province, China, affecting over 8,000 people in 25 countries and territories across ?ve continents. The approach can enable faster, more diverse study enrollments. The structure revealed an overall right hand-like fold composed of a β-sheet core with an extended central loop. Pandit, S.B. Reguera, J.; Gerlach, P.; Cusack, S. Towards a structural understanding of RNA synthesis by negative strand RNA viral polymerases. ; Briese, T.; Brown, P.A. This RNA-free, encapsidation-competent complex is delivered to the active replication site, possibly via the secondary interaction of P with the viral polymerase. A crystal structure of the SARS-CoV N protein revealed a helical assembly of N2b domain dimers that was proposed as a possible structure for the observed helical nucleocapsid filaments in virions. Feature In this study, we expressed the N protein of SARS-CoV-2 and characterized its biochemical properties. Two molecules of the PCTD-bound N290 molecules are colored red and green. and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198. NTD interacts with both the RNA genome and Membrane/Matrix (M) proteins to form virion particles. The structures also revealed that each monomer of N interacts with 3 neighboring N molecules across the nucleocapsid. In Sendai virus, this is 3′ UAA UUUUUU CC*C in which additional Gs may be inserted at C* during mRNA transcription [, Since the viral genome is encapsidated in the nucleocapsid during viral RNA synthesis, interactions of the RNA sequence with the nucleocapsid protein may be involved in regulation of polymerase activities. Rima, B.K. Two RNA polymerase complexes from vesicular stomatitis virus-infected cells that carry out transcription and replication of genome RNA. Raymond, D.D. The N protein is the most highly expressed of the four major coronavirus structural proteins. ; Kolakofsky, D. Chemical modification of nucleotide bases and mRNA editing depend on hexamer or nucleoprotein phase in Sendai virus nucleocapsids. The nucleic acid and capsid together are called nucleocapsid. 6). Song, X.; Shan, H.; Zhu, Y.; Hu, S.; Xue, L.; Chen, Y.; Ding, W.; Niu, T.; Gu, J.; Ouyang, S.; et al. permission provided that the original article is clearly cited. Analogous to the spherical viruses that follow the icosahedral symmetry to assemble .

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