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- PDB-7yw8: Crystal structure of zika E protein -

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Basic information

Entry
Database: PDB / ID: 7yw8
TitleCrystal structure of zika E protein
ComponentsCore protein
KeywordsVIRAL PROTEIN / Flavivirus / Zika virus / neurovirulence / pathogenesis
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, X.X. / Yang, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31770190 China
CitationJournal: To Be Published
Title: Crystal structure of zika E protein
Authors: Wang, X.X. / Yang, Y.X.
History
DepositionAug 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Core protein
B: Core protein
D: Core protein
C: Core protein


Theoretical massNumber of molelcules
Total (without water)178,9834
Polymers178,9834
Non-polymers00
Water2,216123
1
A: Core protein


Theoretical massNumber of molelcules
Total (without water)44,7461
Polymers44,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Core protein


Theoretical massNumber of molelcules
Total (without water)44,7461
Polymers44,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Core protein


Theoretical massNumber of molelcules
Total (without water)44,7461
Polymers44,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Core protein


Theoretical massNumber of molelcules
Total (without water)44,7461
Polymers44,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.572, 134.482, 214.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Core protein


Mass: 44745.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2Z2DVT8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 289.15 K / Method: liquid diffusion
Details: 0.1 M ammonium citrate tribasic pH 7.0, and 12 % (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R 300K-W / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 58187 / % possible obs: 93.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.69 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.17
Reflection shellResolution: 2.49→2.59 Å / Rmerge(I) obs: 0.12 / Num. unique obs: 58078

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTC

4utc


Resolution: 2.5→41.51 Å / SU ML: 0.3895 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.6407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2804 2903 5 %
Rwork0.2573 55175 -
obs0.2585 58078 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.88 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12244 0 0 123 12367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003212504
X-RAY DIFFRACTIONf_angle_d0.605916955
X-RAY DIFFRACTIONf_chiral_restr0.04161916
X-RAY DIFFRACTIONf_plane_restr0.00352179
X-RAY DIFFRACTIONf_dihedral_angle_d12.42864501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.40671200.35352318X-RAY DIFFRACTION83.75
2.54-2.580.4061310.33832560X-RAY DIFFRACTION93.47
2.58-2.630.39731400.32632717X-RAY DIFFRACTION96.68
2.63-2.680.36631440.31562675X-RAY DIFFRACTION98.67
2.68-2.740.36331530.32012749X-RAY DIFFRACTION98.91
2.74-2.790.35421640.31812688X-RAY DIFFRACTION99.1
2.79-2.860.35571180.33292787X-RAY DIFFRACTION99.28
2.86-2.930.37621430.32852738X-RAY DIFFRACTION99.28
2.93-3.010.36221500.32452769X-RAY DIFFRACTION99.59
3.01-3.10.32041320.30392751X-RAY DIFFRACTION99.48
3.1-3.20.31711500.29332734X-RAY DIFFRACTION97.8
3.2-3.310.32771510.28992740X-RAY DIFFRACTION99.28
3.31-3.450.30181540.2752744X-RAY DIFFRACTION98.91
3.45-3.60.30611430.26622763X-RAY DIFFRACTION98.44
3.6-3.790.283850.26321506X-RAY DIFFRACTION53.84
3.79-4.030.27431200.25792327X-RAY DIFFRACTION83.06
4.03-4.340.27461450.22792724X-RAY DIFFRACTION96.34
4.34-4.780.19911430.20182716X-RAY DIFFRACTION96.69
4.78-5.470.22461430.2112730X-RAY DIFFRACTION95.48
5.47-6.880.25461460.24482697X-RAY DIFFRACTION93.92
6.88-41.510.22771280.22322742X-RAY DIFFRACTION90

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