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- PDB-8pae: Structure of the ectodomain of Atypical Porcine Pestivirus E2 at ... -

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Basic information

Entry
Database: PDB / ID: 8pae
TitleStructure of the ectodomain of Atypical Porcine Pestivirus E2 at 1.2A resolution
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Pestivirus / E2 glycoprotein
Function / homology
Function and homology information


ribonuclease T2 activity / host cell membrane / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / : / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm ...ribonuclease T2 activity / host cell membrane / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / : / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / proteolysis / RNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / RNA dependent RNA polymerase, hepatitis C virus ...Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / DEAD box, Flavivirus / Flavivirus DEAD domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesAtypical porcine pestivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsAitkenhead, H. / Stuart, D.I. / EL Omari, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011224/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Structure / Year: 2024
Title: Structural comparison of typical and atypical E2 pestivirus glycoproteins.
Authors: Aitkenhead, H. / Riedel, C. / Cowieson, N. / Rumenapf, H.T. / Stuart, D.I. / El Omari, K.
History
DepositionJun 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2914
Polymers28,4251
Non-polymers8673
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint13 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.124, 101.124, 43.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Genome polyprotein


Mass: 28424.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atypical porcine pestivirus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A1B1M0D5
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M Bis Tris pH 7.8, 0.05 M sodium citrate, 0.05 M magnesium chloride, 25% PEG Smear High

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→26.26 Å / Num. obs: 93856 / % possible obs: 91.26 % / Redundancy: 4.7 % / Biso Wilson estimate: 18.14 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03183 / Rpim(I) all: 0.01563 / Rrim(I) all: 0.03552 / Net I/σ(I): 18.37
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.5973 / Num. unique obs: 2865 / CC1/2: 0.604 / Rpim(I) all: 0.4507 / Rrim(I) all: 0.7534 / % possible all: 56.09

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→26.26 Å / SU ML: 0.1189 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.3602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1797 4574 4.87 %
Rwork0.1504 89282 -
obs0.1518 93856 91.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.74 Å2
Refinement stepCycle: LAST / Resolution: 1.2→26.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 56 160 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661404
X-RAY DIFFRACTIONf_angle_d1.13571919
X-RAY DIFFRACTIONf_chiral_restr0.1119212
X-RAY DIFFRACTIONf_plane_restr0.0083252
X-RAY DIFFRACTIONf_dihedral_angle_d21.9952220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.29151100.25181654X-RAY DIFFRACTION51.88
1.21-1.230.2846780.24021862X-RAY DIFFRACTION55.62
1.23-1.240.2032740.22371952X-RAY DIFFRACTION61.06
1.24-1.260.25041500.22252122X-RAY DIFFRACTION65.32
1.26-1.280.25241160.21622292X-RAY DIFFRACTION69.04
1.28-1.290.20521220.18952460X-RAY DIFFRACTION76.39
1.29-1.310.23151440.18652752X-RAY DIFFRACTION84.43
1.31-1.330.21741800.18532980X-RAY DIFFRACTION92.67
1.33-1.350.18841580.16733098X-RAY DIFFRACTION94.71
1.35-1.370.17991680.163100X-RAY DIFFRACTION96.74
1.37-1.40.17541780.1463254X-RAY DIFFRACTION97.67
1.4-1.420.19761600.15783172X-RAY DIFFRACTION99.52
1.42-1.450.18471620.14783224X-RAY DIFFRACTION98.54
1.45-1.480.18452100.13863244X-RAY DIFFRACTION99.6
1.48-1.510.18091540.12593264X-RAY DIFFRACTION99.02
1.51-1.550.17071520.14653256X-RAY DIFFRACTION98.9
1.55-1.590.16891240.13583282X-RAY DIFFRACTION99.94
1.59-1.630.16151520.13363200X-RAY DIFFRACTION99.35
1.63-1.680.18491460.13083280X-RAY DIFFRACTION99.54
1.68-1.730.18651560.14993242X-RAY DIFFRACTION99.71
1.73-1.790.19741740.14263272X-RAY DIFFRACTION100
1.79-1.860.13991480.13713314X-RAY DIFFRACTION99.83
1.86-1.950.18932060.14533192X-RAY DIFFRACTION99.94
1.95-2.050.17141600.15423286X-RAY DIFFRACTION100
2.05-2.180.14471660.14893240X-RAY DIFFRACTION99.94
2.18-2.350.17261620.15393248X-RAY DIFFRACTION100
2.35-2.580.19042000.16363228X-RAY DIFFRACTION99.94
2.59-2.960.19551800.16953252X-RAY DIFFRACTION100
2.96-3.720.15951320.14583292X-RAY DIFFRACTION100
3.73-26.260.18931520.13823268X-RAY DIFFRACTION99.3

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