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- PDB-8v0h: Structural characterization of zika virus NS2B by NMR and RosettaMP -

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Basic information

Entry
Database: PDB / ID: 8v0h
TitleStructural characterization of zika virus NS2B by NMR and RosettaMP
ComponentsSerine protease subunit NS2B
KeywordsVIRAL PROTEIN / NS2B / membrane protein / viral replication / NS3 protease cofactor
Function / homology
Function and homology information


symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway ...symbiont-mediated suppression of host interferon-mediated signaling pathway / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / protein-macromolecule adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / 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 / lipid binding / viral envelope / GTP binding / 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
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 speciesZika virus
MethodSOLUTION NMR / molecular dynamics
AuthorsPenna, B.R. / Gomes-Neto, F. / Anobom, C.D. / Valente, A.P.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)309893/2022-4 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and dynamics characterization of the Zika virus NS2B using nuclear magnetic resonance and RosettaMP: A challenge for transmembrane protein studies.
Authors: Penna, B.R. / Gomes-Neto, F. / Anobom, C.D. / Valente, A.P.
History
DepositionNov 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease subunit NS2B


Theoretical massNumber of molelcules
Total (without water)17,0861
Polymers17,0861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine protease subunit NS2B / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


Mass: 17085.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: host "Homo sapiens" / Source: (gene. exp.) Zika virus / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q32ZE1
Has protein modificationN

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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 TROSY
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HN(CA)CB
121isotropic13D HN(COCA)CB
161isotropic13D HNCA
171isotropic13D HN(CO)CA

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Sample preparation

DetailsType: micelle
Contents: 20 mM sodium phosphate, 0.1 % w/v sodium dodecyl sulfate, 2 mM beta-mercaptoethanol, 5 mM sodium azide, 100 % [U-2H] D2O
Details: Protein is in SDS micelle / Label: 2H,13C,15N_NS2B / Solvent system: 100 % [U-2H] D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
0.1 % w/vsodium dodecyl sulfatenatural abundance1
2 mMbeta-mercaptoethanolnatural abundance1
5 mMsodium azidenatural abundance1
Sample conditionsDetails: Protein is in SDS micelle / Ionic strength: 0 Not defined / Label: NS2Bsample_condition / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisVersion 2.4.2Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GW.peak picking
CcpNmr Analysis AssignVersion 2.4.2Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GW.chemical shift assignment
CcpNmr AnalysisVersion 2.4.2Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GW.data analysis
CS-ROSETTAShen, Vernon, Baker and Baxchemical shift calculation
Rosetta2020.08.61146Yarov-Yarovoy V, Schonbrun J, Baker D.structure calculation
Rosetta2020.08.61146ivon LG, Moretti R, Baker Drefinement
Rosetta2020.08.61146ivon LG, Moretti R, Baker Dgeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 7
Details: selection based on rosetta chemical shif potential and total energy
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500000 / Conformers submitted total number: 20

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