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- PDB-5omz: Solution structure of domain III (DIII)of Zika virus Envelope protein -

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Database: PDB / ID: 5omz
TitleSolution structure of domain III (DIII)of Zika virus Envelope protein
DescriptorEnvelope Protein
KeywordsVIRAL PROTEIN / ZIKA virus Envelope protein domain / ZIKV
Specimen sourceZika virus (strain Mr 766) / virus / ZIKV
MethodSolution NMR (Simulated annealing)
AuthorsZerbe, O. / Bardelli, M.
CitationCell, 2017, 171, 229-241.e15

Cell, 2017, 171, 229-241.e15 Yorodumi Papers
A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential.
Wang, J. / Bardelli, M. / Espinosa, D.A. / Pedotti, M. / Ng, T.S. / Bianchi, S. / Simonelli, L. / Lim, E.X.Y. / Foglierini, M. / Zatta, F. / Jaconi, S. / Beltramello, M. / Cameroni, E. / Fibriansah, G. / Shi, J. / Barca, T. / Pagani, I. / Rubio, A. / Broccoli, V. / Vicenzi, E. / Graham, V. / Pullan, S. / Dowall, S. / Hewson, R. / Jurt, S. / Zerbe, O. / Stettler, K. / Lanzavecchia, A. / Sallusto, F. / Cavalli, A. / Harris, E. / Lok, S.M. / Varani, L. / Corti, D.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 2, 2017 / Release: Oct 4, 2017

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Deposited unit
A: Envelope Protein

Theoretical massNumber of molelcules
Total (without water)12,4791

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)9230
NMR ensembles
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy


#1: Polypeptide(L)Envelope Protein

Mass: 12479.393 Da / Num. of mol.: 1 / Fragment: DOMAIN DIII, UNP residues 585-699 / Source: (gene. exp.) Zika virus (strain Mr 766) / virus / References: UniProt: A0A1V0E2E5

Cellular component

Molecular function

Biological process

  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • induction by virus of host autophagy (GO: 0039520)
  • suppression by virus of host STAT2 activity (GO: 0039564)
  • suppression by virus of host type I interferon-mediated signaling pathway (GO: 0039502)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)

Experimental details


ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions IDExperiment IDSolution IDSample stateSpectrometer IDType
111isotropic12D 1H-15N HSQC
1151isotropic22D 1H-13C HSQC aliphatic
1161isotropic22D 1H-13C HSQC aromatic
151isotropic23D HNCO
1101isotropic23D HN(CA)CO
131isotropic23D CBCA(CO)NH
141isotropic23D HNCACB
1121isotropic23D HCCH-TOCSY
1141isotropic23D H(C)CH
1111isotropic23D HBHA(CO)NH
191isotropic23D 1H-15N NOESY
181isotropic23D 1H-13C NOESY aliphatic
171isotropic23D 1H-13C NOESY aromatic
122isotropic22D 1H-15N HSQC
162isotropic23D 1H-15N NOESY
1132isotropic23D HNCO

Sample preparation

NMR sample details
TypeSolution IDContentsDetailsLabelSolvent system
solution1800 uM 15N,13C ZIKA Envelope DIII, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2Osample for resonance assignment and structure determinationsample_H2O90% H2O/10% D2O
solution2400 uM 2H,13C,15N ZIKA Envelope DIII, 20 mM sodium phosphate, 50 mM sodium chloride, 440 uM ZKA190 Fab, 90% H2O/10% D2Operdeuterated 13C,15N samplesample for mapping90% H2O/10% D2O
NMR experiment sample
Conc.UnitsComponentIsotopic labelingSolution ID
800uMZIKA Envelope DIII15N,13C1
20mMsodium phosphatenatural abundance1
50mMsodium chloridenatural abundance1
400uMZIKA Envelope DIII2H,13C,15N2
20mMsodium phosphatenatural abundance2
50mMsodium chloridenatural abundance2
440uMZKA190 Fabnatural abundance2
NMR experiment sample conditionsIonic strength: 0.27 / Ionic strength units: mM / Label: conditions_1 / pH: 6 / PH units: pH / Pressure: 1 Pa / Pressure units: atm / Temperature: 300 kelvins / Temperature units: K

NMR measurement

NMR spectrometer
ManufacturerModelField strengthSpectrometer ID


NMR software
TOPSPIN2.1Bruker Biospinprocessing
CARA1.93Keller and Wuthrichchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
NMR refineMethod: simulated annealing / Software ordinal: 5 / Details: further refinement in AMBER
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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