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- PDB-7sgt: Domain III (EDIII) of the POWV E glycoprotein -

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Basic information

Entry
Database: PDB / ID: 7sgt
TitleDomain III (EDIII) of the POWV E glycoprotein
ComponentsEnvelope protein E
KeywordsVIRAL PROTEIN / Powassan virus / nanoparticle immunogen / flavivirus / monoclonal antibody
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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell ...: / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 powassan virus
MethodSOLUTION NMR / simulated annealing
AuthorsHarris, R. / Cahill, S.M. / Cowburn, D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI164047 United States
National Institutes of Health/Office of the DirectorS10DO16305 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA01330 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM1111135 United States
CitationJournal: Plos Pathog. / Year: 2022
Title: A Powassan virus domain III nanoparticle immunogen elicits neutralizing and protective antibodies in mice.
Authors: Malonis, R.J. / Georgiev, G.I. / Haslwanter, D. / VanBlargan, L.A. / Fallon, G. / Vergnolle, O. / Cahill, S.M. / Harris, R. / Cowburn, D. / Chandran, K. / Diamond, M.S. / Lai, J.R.
History
DepositionOct 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope protein E


Theoretical massNumber of molelcules
Total (without water)11,1831
Polymers11,1831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Envelope protein E


Mass: 11182.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne powassan virus (strain lb) / Strain: LB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04538
Has protein modificationY

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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
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-15N TOCSY
141isotropic1HNHA
252isotropic22D 1H-15N HSQC
363isotropic22D 1H-13C HSQC aliphatic
373isotropic33D 1H-13C NOESY
383isotropic23D 1H-13C NOESY aromatic
3163isotropic313C HSQC aro
292isotropic33D HNCO
2102isotropic23D HN(CO)CA
2112isotropic23D HNCA
2132isotropic23D HN(COCA)CB
2122isotropic2HN(CA)CB
2142isotropic2HN(CO)NH TOCSY
3153isotropic2HC(CO)NH TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1.5 mM [U-15N] domain III (EDIII) of the POWV E glycoprotein, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O~0.5mM 15N-labelled DIII in 20mM NaP pH6.2, 50mM NaCl, TSP, 10% D2O, 3mm tube15N sample90% H2O/10% D2O
solution21 mM [U-15N] domain III (EDIII) of the POWV E glycoprotein, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O~1.0mM 15N/13C-labelled DIII in 20mM NaP pH6.2, 50mM NaCl15N / 13C sample95% H2O/5% D2O
solution31 mM [U-15N] domain III (EDIII) of the POWV E glycoprotein, 20 mM sodium phosphate, 50 mM sodium chloride, 100% D2O~1.0mM 15N/13C-labelled DIII in 20mM NaP pH6.2, 50mM NaCl, TSP15N / 13C sample D20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
.5 mMdomain III (EDIII) of the POWV E glycoprotein[U-15N]1
20 mMsodium phosphatenone1
50 mMsodium chloridenone1
1 mMdomain III (EDIII) of the POWV E glycoprotein[U-15N]2
20 mMsodium phosphatenone2
50 mMsodium chloridenone2
1 mMdomain III (EDIII) of the POWV E glycoprotein[U-15N]3
20 mMsodium phosphatenone3
50 mMsodium chloridenone3
Sample conditions

Ionic strength: 70 mM / Ionic strength err: 1 / Label: cond 1 / PH err: 0.1 / Pressure: 1 atm / Pressure err: _ / Temperature err: 0.1

Conditions-IDDetailspHTemperature (K)
1pH 6.2 298 K6.2 pH*298 K
3pH 6.2 278 K6.2 pD278 K
2pH 6.2 278 K6.2 pH*278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD6001Einstein
Bruker AVANCE DMXBrukerAVANCE DMX8002NYSBC
Bruker AVANCE III HDBrukerAVANCE III HD7003NYSBC

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.3Bruker Biospinprocessing
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.4CCPNchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
SideRhttps://www.ucl.ac.uk/hansen-lab/sider_dfhstructure calculation
X-PLOR NIH3.42Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr Analysis2CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 8
Details: Used Xplor-NIH 3.2: Final refinement with the inclusion of specific water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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