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- PDB-6c44: Zika virus capsid protein -

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Basic information

Entry
Database: PDB / ID: 6c44
TitleZika virus capsid protein
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / zika virus / capsid / RNA binding protein
Function / homology
Function and homology information


: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane ...: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Arc Repressor Mutant, subunit A - #930 / 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 ...Arc Repressor Mutant, subunit A - #930 / 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 / Arc Repressor Mutant, subunit A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesZika virus
MethodSOLUTION NMR / molecular dynamics
AuthorsMorando, M.A. / Barbosa, G.M. / Cruz-Oliveira, C. / Da Poian, A.T. / Almeida, F.C.L.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Capes-CDT FIOCRUZCapes-CDTS-Fiocruz (001/2012) Brazil
FAPERJ215141, 210361, 204432, 201167, 201316 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)209306/2013-2, 457773/2014-6, 306669/2013-7 Brazil
FINEP0267/16 Brazil
CitationJournal: Biochemistry / Year: 2019
Title: Dynamics of Zika Virus Capsid Protein in Solution: The Properties and Exposure of the Hydrophobic Cleft Are Controlled by the alpha-Helix 1 Sequence.
Authors: Morando, M.A. / Barbosa, G.M. / Cruz-Oliveira, C. / Da Poian, A.T. / Almeida, F.C.L.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 31, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_nmr_spectrometer.model
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 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: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)23,3532
Polymers23,3532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3500 Å2
ΔGint-45 kcal/mol
Surface area8840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Capsid protein


Mass: 11676.451 Da / Num. of mol.: 2 / Fragment: UNP residues 1-104
Source method: isolated from a genetically manipulated source
Details: protein id AMD16557.1 / Source: (gene. exp.) Zika virus / Strain: Mr 766 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A0A1V0E2H9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CA)CO
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic12D 1H-15N HSQC
191isotropic13D 1H-15N NOESY
1101isotropic23D 1H-13C NOESY aliphatic
1111isotropic23D 1H-13C NOESY aromatic
1121isotropic22D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-99% 13C; U-99% 15N] ZIKVC, 90% H2O/10% D2O
Details: 55 mM sodium phosphate buffer, 200 mM NaCl, 5 mM azide, 2 mM PMSF, 5 mM EDTA
Label: 15N_13C_ZIKVC / Solvent system: 90% H2O/10% D2O
SampleConc.: 300 uM / Component: ZIKVC / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.2323 M / Label: unique conditions / pH: 6 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE III HDBrukerAVANCE III HD9002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNMR2.4.2CCPNchemical shift assignment
CcpNMR2.4.2CCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: With explicit water shell
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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