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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 proteinCapsid
KeywordsVIRAL PROTEIN / zika virus / capsid / RNA binding protein
Function / homologyFlavivirus glycoprotein central and dimerisation domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus capsid protein C / Flaviviral glycoprotein E, central domain, subdomain 1 ...Flavivirus glycoprotein central and dimerisation domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus capsid protein C / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Helicase superfamily 1/2, ATP-binding domain / Genome polyprotein, Flavivirus / Immunoglobulin E-set / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus glycoprotein E, immunoglobulin-like domain / P-loop containing nucleoside triphosphate hydrolase / S-adenosyl-L-methionine-dependent methyltransferase / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus capsid protein C superfamily / Flaviviral glycoprotein E, dimerisation domain / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus polyprotein propeptide superfamily / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus non-structural Protein NS1 / Peptidase S7, Flavivirus NS3 serine protease / Helicase, C-terminal / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS2B / Flavivirus polyprotein propeptide / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus capsid protein C / FtsJ-like methyltransferase / Flavivirus non-structural protein NS4A / Envelope glycoprotein M, flavivirus / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4A / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS4B / Flavivirus RNA-directed RNA polymerase / suppression by virus of host innate immune response / host cell endoplasmic reticulum / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / ATP-dependent helicase activity / host cell membrane / RNA helicase activity / double-stranded RNA binding / viral capsid / induction by virus of host autophagy / viral RNA genome replication / fusion of virus membrane with host endosome membrane / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / ATP binding / metal ion binding / Genome polyprotein
Function and homology information
Specimen sourceZika virus
MethodSOLUTION NMR / molecular dynamics
AuthorsMorando, M.A. / Barbosa, G.M. / Cruz-Oliveira, C. / Da Poian, A.T. / Almeida, F.C.L.
CitationJournal: To be Published
Title: Zika virus capsid protein
Authors: Morando, M.A. / Barbosa, G.M. / Cruz-Oliveira, C. / Da Poian, A.T. / Almeida, F.C.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 11, 2018 / Release: Jan 16, 2019

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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
Polyers23,3532
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)3500
ΔGint (kcal/M)-45
Surface area (Å2)8840
NMR ensembles
Datacriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Capsid protein / Capsid


Mass: 11676.451 Da / Num. of mol.: 2 / Fragment: UNP residues 1-104 / Source: (gene. exp.) Zika virus / Details: protein id AMD16557.1 / Strain: Mr 766 / Plasmid name: 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 HNCACB
151isotropic13D CBCA(CO)NH
161isotropic13D HBHA(CO)NH
171isotropic13D HCCH-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: 6.0 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strengthSpectrometer ID
Bruker AvanceIIIBrukerAvanceIII6001
Bruker AvanceIIIHDBrukerAvanceIIIHD9002

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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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