Abstract:
:Nervous necrosis virus (NNV) is a non-enveloped virus that causes massive mortality in aquaculture fish production worldwide. Recently X-ray crystallography and single particle cryo-EM have independently determined the icosahedral capsid of NNV to near-atomic resolutions to show the capsid protein is composed of a S-domain (shell) and a P-domain (protrusion) connected by a linker. However, the structure of the spike on NNV capsid made of trimeric P-domains was poorly resolved by cryo-EM. In addition, comparing the spike in the cryo-EM with that by X-ray suggests that the P-domain can move drastically relative to the shell, implicating an underlying structural mechanism during the infectious process. Yet, it remains unclear that such structural re-arrangement is ascribed to the change of the conformation of individual P-domain or in the association among P-domains. Given that molecular structure of the P-domain in solution phase is still lacking, we aim to determine the structure of the P-domain by solution NMR spectroscopy. In this communication, we report backbone and side chain 1H, 13C and 15N chemical shifts of the P-domain (residues 221-338) together with the linker region (residues 214-220), revealing ten β-strands via chemical shift propensity analysis. Our findings are consistent with the X-ray crystal structure of the P-domain reported elsewhere. The current study provides a framework towards further structural analyses of the P-domain in various solution conditions.
journal_name
Biomol NMR Assignjournal_title
Biomolecular NMR assignmentsauthors
Štěrbová P,Wu D,Lou YC,Wang CH,Chang WH,Tzou DMdoi
10.1007/s12104-019-09921-xsubject
Has Abstractpub_date
2020-04-01 00:00:00pages
63-66issue
1eissn
1874-2718issn
1874-270Xpii
10.1007/s12104-019-09921-xjournal_volume
14pub_type
杂志文章abstract::The Src tyrosine kinase is the paradigm of an oncogenic kinase, and of regulation by intramolecular inhibitory interactions, as well as an important anticancer target due to its roles in cell proliferation and metastasis. The assignment of backbone (1)H(N), (13)C(α), (13)CO, and (15)N, and sidechain (13)C(β) resonance...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-011-9304-7
更新日期:2011-10-01 00:00:00
abstract::The bacterium Geobacter metallireducens is capable of transferring electrons to the cell exterior, a process designated extracellular electron transfer. This mechanism allows the microorganism to reduce extracellular acceptors such as Fe(III) (hydr)oxides and water toxic and/or radioactive contaminants including Cr(VI...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-019-09916-8
更新日期:2020-04-01 00:00:00
abstract::KKT4 is a kinetoplastid-specific microtubule-binding kinetochore protein that lacks significant similarity to any known kinetochore or microtubule-binding proteins. Here we present the 1H, 13C and 15N resonance assignments for several fragments from the microtubule-binding domain of KKT4 (KKT4115-343) from Trypanosoma...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-020-09968-1
更新日期:2020-10-01 00:00:00
abstract::The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of many important proteins during embryonic morphogenesis. We report complete NMR chemical shift assignments of the mouse HOXA13 DNA binding domain (A13DBD; BMRB no. 16252). ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-009-9174-4
更新日期:2009-12-01 00:00:00
abstract::NOXO1 (Nox Organizer 1) is a homolog of the NAPDH oxidase protein p47(phox). NADPH oxidases transfer electrons from NADPH to molecular oxygen, generating the superoxide anion. NOXO1 contains an N-terminal PX (phox homology) domain and is one of several PX domain-containing proteins found in the cytosolic subunits of t...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-010-9286-x
更新日期:2011-10-01 00:00:00
abstract::The apo-form of the 21.4 kDa catalytic domain and the 10.7 kDa carbohydrate binding domain of the AA10 family lytic polysaccharide monooxygenase ScLPMO10C from Streptomyces coelicolor have been isotopically labeled and recombinantly expressed in Escherichia coli. In this paper, we report the 1H, 13C, and 15N chemical ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-017-9759-2
更新日期:2017-10-01 00:00:00
abstract::Parkinson's disease (PD) is a chronic, progressive neurodegenerative disease, where dopaminergic cells die most prominently in the area of substantia nigra. Neurotrophic factors (NTFs) are secreted proteins, which upon binding to their target receptors trigger survival pathways to prevent neuronal loss. Recently disco...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-010-9251-8
更新日期:2010-10-01 00:00:00
abstract::We report NMR assignments of the protein backbone of the C-terminal domain (163 a.a.) of human class 1 translation termination factor eRF1. It was found that several protein loop residues exist in two slowly interconverting conformational states. ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-007-9050-z
更新日期:2007-12-01 00:00:00
abstract::RegB is involved in the control of the phage T4 life cycle. It inactivates the phage early mRNAs when their translation is no more required. We determined its structure and identified residues involved in substrate binding. For this, all backbone and 90% of side-chain resonance frequencies were assigned. ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-007-9021-4
更新日期:2007-07-01 00:00:00
abstract::Snu13p is a highly conserved RNA binding protein from Saccharomyces cerevisiae required for both eukaryotic pre-mRNA splicing and pre-rRNA processing. The 1H, 13C, and 15N assignments were determined from multidimensional, multinuclear NMR experiments conducted at 25 degrees C. ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-007-9069-1
更新日期:2008-06-01 00:00:00
abstract::Latent TGFβ binding protein 1 (LTBP1) is a large extracellular protein that has been shown to bind covalently to the propeptide of TGFβ cytokines and form a large latent complex, which is then incapable of binding TGFβ receptors. LTBP1 has also been demonstrated to interact with a number of insoluble extracellular mat...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-013-9474-6
更新日期:2014-04-01 00:00:00
abstract::Human heterogeneous nuclear ribonucleoprotein H (hnRNP H) regulates alternative splicing of HIV-1 Tat pre-mRNA. The structure of the first N-terminal domain (residues 1-104) of hnRNP H was solved and its binding to an exonic splicing silencer (pESS2) studied. For this, all backbone and 85% of side-chain resonance freq...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-007-9061-9
更新日期:2007-12-01 00:00:00
abstract::E. coli nitroreductase NfsB (also called NfnB) has been studied extensively, largely due to its potential for cancer gene therapy. A homodimeric flavoprotein of 216 residues, it catalyses the reduction of nitroaromatics to cytotoxic hydroxylamines by NADH and NADPH and also the reduction of quinones to hydroxyquinones...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-020-09997-w
更新日期:2021-01-09 00:00:00
abstract::Bacillus subtilis ATCC 6633 produces the lipid II targeting lantibiotic subtilin. For self-protection these gram-positive bacteria express a cluster of four self-immunity proteins named SpaIFEG. SpaI is a 16.8 kDa lipoprotein which is attached to the outside of the cytoplasmic membrane via a covalently linked diacylgl...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-011-9314-5
更新日期:2012-04-01 00:00:00
abstract::The Breast Cancer susceptibility protein 2 (BRCA2) is involved in mechanisms that maintain genome stability, including DNA repair, replication and cell division. These functions are ensured by the folded C-terminal DNA binding domain of BRCA2 but also by its large regions predicted to be disordered. Several studies ha...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-019-09924-8
更新日期:2020-04-01 00:00:00
abstract::Bacterial thiol peroxidases (Tpxs) are antioxidant enzymes which exist in various bacteria. Tpxs reduce the lipid hydroperoxides to protect the membrane lipid from destruction by reactive oxygen species. Tpxs are essential enzymes for bacterial anaerobic growth. Herein, we report the resonance assignments of (1)H, (13...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-008-9116-6
更新日期:2008-12-01 00:00:00
abstract::Immunoglobulin E (IgE) plays a central role in allergic reactions. IgE is a dynamic molecule that is capable of undergoing large conformational changes. X-ray crystal structures of the Fc region of IgE in complex with various ligands have shown that IgE-Fc can exist in extended and various bent conformations. IgE-Fc c...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-020-09936-9
更新日期:2020-04-01 00:00:00
abstract::Early response to dehydration 10 protein (ERD10) is an intrinsically disordered protein from Arabidopsis thaliana. The protein is upregulated during stress however its mechanism of action at atomic level is not well understood. In the present work multidimensional NMR methodologies are used in order to facilitate the ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-017-9732-0
更新日期:2017-10-01 00:00:00
abstract::YbeA is a 3-methylpseudoridine methyltransferase from Escherichia coli that forms a stable homodimer in solution. It is one of the deeply trefoil 31 knotted proteins, of which the knot encompasses the C-terminal helix that threads through a long loop. Recent studies on the knotted protein folding pathways using YbeA h...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-013-9501-7
更新日期:2014-10-01 00:00:00
abstract::Nuclear Factor κB (NF-κB) is a family of five related transcription factors that recognize a κB DNA element on the promoter and enhancer regions of target genes and modulate their expression. Here we report a complete set of 1H, 13C, 15N backbone and side chain resonance assignments for the p50 DNA binding and dimeriz...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-020-09978-z
更新日期:2020-09-16 00:00:00
abstract::Translation initiation factor 3 (IF3) is one of the three protein factors that bind to the small ribosomal subunit and it is required for the initiation of protein biosynthesis in bacteria. IF3 contains two independent domains, N- and C-terminal domains, which are connected by a lysine-rich interdomain linker. IF3 und...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-020-09926-x
更新日期:2020-04-01 00:00:00
abstract::Norovirus protease cleaves the virus-encoded polyprotein into six mature nonstructural proteins, presenting itself as an essential enzyme for the viral replication as well as an attractive target for the antiviral drug development. A deeper understanding of the structural mechanism of the protease-substrates/inhibitor...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-011-9316-3
更新日期:2012-04-01 00:00:00
abstract::The S100 family belongs to the EF-hand calcium-binding proteins regulating a wide range of important cellular processes via protein-protein interactions. Most S100 proteins adopt a conformation of non-covalent homodimer for their functions. Calcium binding to the EF-hand motifs of S100 proteins is essential for trigge...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-012-9412-z
更新日期:2013-10-01 00:00:00
abstract::Translationally-controlled tumor protein (TCTP) is a eukaryote-conserved protein with crucial roles in cellular growth. It has also been proposed that plant TCTP has functions specific to plant, while no structure of TCTP from photosynthetic organism has been reported. Nannochloropsis is a photosynthetic microalga wit...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-015-9602-6
更新日期:2015-10-01 00:00:00
abstract::The peptidoglycan is a major component of the bacterial cell wall and is essential to maintain cellular integrity and cell shape. Penicillin-Binding Proteins (PBPs) catalyze the final biosynthetic steps of peptidoglycan synthesis from lipid II precursor and are the main targets of β-lactam antibiotics. The molecular d...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-014-9546-2
更新日期:2015-04-01 00:00:00
abstract::We report the (1)H, (13)C, and (15)N chemical shift assignments of both oxidized and reduced forms of an abundant periplasmic c-type cytochrome, designated ApcA, isolated from the acidophilic gram-negative facultatively anaerobic metal-reducing alphaproteobacterium Acidiphilium cryptum. These resonance assignments pro...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-010-9274-1
更新日期:2011-04-01 00:00:00
abstract::Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-015-9603-5
更新日期:2015-10-01 00:00:00
abstract::RpsA, also known as ribosomal protein S1, is an essential protein required for translation initiation of mRNAs when their Shine-Dalgarno sequence is degenerated (Sorensen et al. 1998). In addition, RpsA of Mycobacterium tuberculosis (M. tb) is involved in trans-translation, which is an effective system mediated by tmR...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-017-9734-y
更新日期:2017-10-01 00:00:00
abstract::Fibroblast growth factor receptor (FGFR) 4 has been associated with progression of melanoma, breast, head and neck and hepatocellular carcinoma and is therefore an interesting target for therapeutic intervention (Ho et al. in J Hepatol 50:118-127, 2009). The extracellular D2 domain of the FGFR4 receptor contains a hep...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-012-9405-y
更新日期:2013-10-01 00:00:00
abstract::The agglutinin-like-sequence (ALS) family of adhesion proteins are a key virulence factor for C. albicans. These proteins have been implicated in several functions, notably adhesion and invasion of different cell types, as well as binding to peptides and proteins in the cell surface and extracellular matrix. In order ...
journal_title:Biomolecular NMR assignments
pub_type: 杂志文章
doi:10.1007/s12104-010-9243-8
更新日期:2010-10-01 00:00:00