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- PDB-7e4k: WNV envelope protein -

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Basic information

Entry
Database: PDB / ID: 7e4k
TitleWNV envelope protein
ComponentsCore protein
KeywordsVIRAL PROTEIN / West Nile Virus / Envelope protein
Function / homology
Function and homology information


: / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity ...: / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 / RNA helicase / 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 / structural molecule activity / virion membrane / 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 speciesWest Nile virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsXiao, H. / Qi, J. / Huang, C. / Song, J. / Cheng, H.
CitationJournal: To Be Published
Title: WNV envelope protein
Authors: Xiao, H. / Qi, J.
History
DepositionFeb 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 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


Theoretical massNumber of molelcules
Total (without water)43,6351
Polymers43,6351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19820 Å2
Unit cell
Length a, b, c (Å)74.795, 34.930, 93.672
Angle α, β, γ (deg.)90.000, 112.994, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 43634.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Production host: Escherichia coli (E. coli)
References: UniProt: F1D832, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M NaI, 0.1 M Bis Tris propane, 20% w/v PEG 3350, 10 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 372171 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 39.93 Å2 / CC1/2: 0.989 / Net I/σ(I): 17.6
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 12609 / CC1/2: 0.951 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hg0

2hg0


Resolution: 2.69→45.79 Å / SU ML: 0.4046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288 573 5.09 %
Rwork0.2603 10688 -
obs0.2617 11261 88.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.09 Å2
Refinement stepCycle: LAST / Resolution: 2.69→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 0 0 3043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513108
X-RAY DIFFRACTIONf_angle_d0.86524219
X-RAY DIFFRACTIONf_chiral_restr0.0516481
X-RAY DIFFRACTIONf_plane_restr0.0045542
X-RAY DIFFRACTIONf_dihedral_angle_d17.95961111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.960.3746960.32821773X-RAY DIFFRACTION59.66
2.96-3.390.31721700.30662822X-RAY DIFFRACTION95.41
3.39-4.270.30041510.25283046X-RAY DIFFRACTION99.81
4.27-45.790.24511560.23023047X-RAY DIFFRACTION97.24
Refinement TLS params.Method: refined / Origin x: -17.7063218689 Å / Origin y: 0.742835035225 Å / Origin z: -20.2388481988 Å
111213212223313233
T0.0828340633014 Å2-0.0492860405536 Å20.015124581494 Å2-0.0865168076418 Å20.082883136477 Å2--0.0587504469568 Å2
L0.142382283671 °20.0693547423474 °20.00901917462994 °2-0.120087920741 °2-0.0827895541644 °2--0.108041561588 °2
S0.0235242030825 Å °0.174834203713 Å °0.0282618860512 Å °-0.0661909606002 Å °0.0997604380701 Å °-0.008912734714 Å °0.0125235258538 Å °-0.166821309612 Å °0.170110834217 Å °
Refinement TLS groupSelection details: all

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