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- PDB-8ynj: Crystal structure of Langat virus helicase -

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Basic information

Entry
Database: PDB / ID: 8ynj
TitleCrystal structure of Langat virus helicase
ComponentsSerine protease NS3
KeywordsVIRAL PROTEIN / helicase / Langat virus / viperin / antiviral drugs
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / : / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / : / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / : / Flavivirus NS3 helicase, C-terminal helical domain / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 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 speciesLangat virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsChen, C. / Xue, L.R.
Funding support China, 1items
OrganizationGrant numberCountry
Other government21JCQNJC01890 China
CitationJournal: To Be Published
Title: Crystal structure of Langat virus helicase
Authors: Chen, C. / Xue, R.L.
History
DepositionMar 11, 2024Deposition site: PDBJ / Processing site: PDBC
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
A: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)50,3461
Polymers50,3461
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.018, 68.018, 213.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Serine protease NS3 / Flavivirin protease NS3 catalytic subunit / Non-structural protein 3


Mass: 50346.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langat virus (strain TP21) / Production host: Escherichia coli (E. coli)
References: UniProt: P29837, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 49.76 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium malonate pH 7.0, 17% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.48→49.13 Å / Num. obs: 18766 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 68.73 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.8
Reflection shellResolution: 2.48→2.61 Å / Num. unique obs: 2670 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→36.12 Å / SU ML: 0.3168 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2802 930 4.99 %
Rwork0.2384 17720 -
obs0.2404 18650 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.2 Å2
Refinement stepCycle: LAST / Resolution: 2.48→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 13 3461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00143523
X-RAY DIFFRACTIONf_angle_d0.38044771
X-RAY DIFFRACTIONf_chiral_restr0.0399509
X-RAY DIFFRACTIONf_plane_restr0.0035631
X-RAY DIFFRACTIONf_dihedral_angle_d20.04981318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.610.32891330.27122467X-RAY DIFFRACTION100
2.61-2.770.35561280.30692471X-RAY DIFFRACTION100
2.77-2.980.36121430.30792491X-RAY DIFFRACTION100
2.98-3.280.31071260.29312490X-RAY DIFFRACTION99.96
3.28-3.760.34081230.27952501X-RAY DIFFRACTION98.65
3.76-4.730.24781350.21622560X-RAY DIFFRACTION99.93
4.74-36.120.24571420.2052740X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38293490451-0.123113439236-0.3114722250592.47674142630.3314271819742.741420032790.004522738094940.465265477029-0.2014995878370.336437511669-0.121028645941-0.246226052450.2094915326160.1721214855390.1130606758080.6146365758460.00163628738418-0.1870222807340.387419486788-0.01520577641730.536691812369-22.258420059814.78839893138.5230453378
28.064897722624.794199810531.859690469248.60684014977-2.937345180873.37558669358-0.2797743333790.6203183048481.055827061230.166172567420.09442410416230.616690705038-0.5964668260060.3085994946460.1052317173140.594649866420.153467224618-0.1057343575260.6144700469050.01673830674490.621268407073-22.869277349725.8503045547-2.55349746924
31.94393885722-0.6099818252620.5649698637892.933659994640.9019131002093.40385028710.000898791552148-0.2793293911210.154906295841.289660264780.0382470082203-0.4675464313410.501292770829-0.240023625250.1150409334191.3688590695-0.0451292641281-0.3793726647610.4034187387910.06161598809050.827623702283-18.476610396615.189099873431.1611244233
47.78997102508-1.35825176575-1.534697902437.52731013287-0.3498768784176.49870095511-0.1076662943940.2878639545160.15020733285-0.02304928324490.0567133685780.7805185268170.0311941650656-0.3865007248050.1088960346920.596027990706-0.0487684190601-0.07566962135820.402833698588-0.02607875857990.507424866047-45.739806166324.563216088318.7861464083
54.73942267817-1.5063993221-2.893996961061.299634334131.051880682232.07704022615-0.383755949510.160709614974-0.403630443430.52358687113-0.002979985197430.3121732781270.5778306357870.05858217105140.2886081513040.8827342695620.00212740213114-0.05964296802440.493604829648-0.05608462864980.843027303794-36.848420081214.597304846612.6756681112
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 280 through 416 )280 - 416266 - 402
22chain 'A' and (resid 417 through 447 )417 - 447403 - 433
33chain 'A' and (resid 5 through 156 )5 - 1561 - 142
44chain 'A' and (resid 157 through 244 )157 - 244143 - 230
55chain 'A' and (resid 245 through 279 )245 - 279231 - 265

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