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- PDB-7ywq: Solution structure of homodimeric Capsid protein (residues 17-95)... -

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Basic information

Entry
Database: PDB / ID: 7ywq
TitleSolution structure of homodimeric Capsid protein (residues 17-95) of Tick-borne encephalitis virus (d16-TBEVC)
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Capsid protein / Homodimer / Tick-borne encephalitis virus
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesTick-borne encephalitis virus
MethodSOLUTION NMR / simulated annealing
AuthorsNovotny, R.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Tick-borne encephalitis virus capsid protein induces translational shutoff as revealed by its structural-biological analysis.
Authors: Selinger, M. / Novotny, R. / Sys, J. / Roby, J.A. / Tykalova, H. / Ranjani, G.S. / Vancova, M. / Jaklova, K. / Kaufman, F. / Bloom, M.E. / Zdrahal, Z. / Grubhoffer, L. / Forwood, J.K. / ...Authors: Selinger, M. / Novotny, R. / Sys, J. / Roby, J.A. / Tykalova, H. / Ranjani, G.S. / Vancova, M. / Jaklova, K. / Kaufman, F. / Bloom, M.E. / Zdrahal, Z. / Grubhoffer, L. / Forwood, J.K. / Hrabal, R. / Rumlova, M. / Sterba, J.
History
DepositionFeb 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)17,7402
Polymers17,7402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Detection of protein dimerization by a size-exclusion chromatography., cross-linking, Further confirmation of protein dimerization., mass spectrometry, Identification of ...Evidence: gel filtration, Detection of protein dimerization by a size-exclusion chromatography., cross-linking, Further confirmation of protein dimerization., mass spectrometry, Identification of unique linkages from chemical cross-linking by mass spectrometry (XL-MS). Identification of interaction interfaces by hydrogen-deuterium exchange experiment (HDX-MS).
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2400 Å2
ΔGint-13 kcal/mol
Surface area12050 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Genome polyprotein


Mass: 8869.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus / Strain: Neudoerfl / Plasmid: pET22B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P14336

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HCACO
151isotropic13D HNCA
161isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-99% 13C; U-99% 15N] d16-TBEVC, 50 mM NaCl, 50 mM sodium phosphate, 5 % glycerol, 95% H2O/5% D2O
Label: 13C_15N_d16TBEVC / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMd16-TBEVC[U-99% 13C; U-99% 15N]1
50 mMNaClnone1
50 mMsodium phosphatenone1
5 %glycerolnone1
Sample conditionsIonic strength: 100 mM / Label: Conditions / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
CcpNmr Analysis2.5.2CCPNdata analysis
CcpNmr Analysis2.5.2CCPNpeak picking
CcpNmr Analysis2.5.2CCPNchemical shift assignment
X-PLOR NIH3.2Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH3.2Schwieters, Kuszewski, Tjandra and Clorerefinement
HADDOCK2.2Bonvinprocessing
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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