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- PDB-6urv: Crystal structure of Yellow Fever Virus NS2B-NS3 protease domain -

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Basic information

Entry
Database: PDB / ID: 6urv
TitleCrystal structure of Yellow Fever Virus NS2B-NS3 protease domain
Components
  • NS2B
  • NS3 protease
KeywordsVIRAL PROTEIN / Yellow fever / protease / NS3 / flavivirus flaviviruses / YFV / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


flavivirin / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / methyltransferase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / methylation / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...flavivirin / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / methyltransferase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / methylation / 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 / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / 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 ...Thrombin, subunit H - #120 / 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 / Trypsin-like serine proteases / 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 / Thrombin, subunit H / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Core protein / Core protein / Core protein
Similarity search - Component
Biological speciesYellow fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNoske, G.D. / Gawriljuk, V.F.O. / Fernandes, R.S. / Oliva, G. / Godoy, A.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Structural characterization and polymorphism analysis of the NS2B-NS3 protease from the 2017 Brazilian circulating strain of Yellow Fever virus.
Authors: Noske, G.D. / Gawriljuk, V.O. / Fernandes, R.S. / Furtado, N.D. / Bonaldo, M.C. / Oliva, G. / Godoy, A.S.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 5, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS2B
H: NS3 protease
G: NS2B
E: NS2B
F: NS3 protease
C: NS2B
D: NS3 protease
B: NS3 protease


Theoretical massNumber of molelcules
Total (without water)97,5248
Polymers97,5248
Non-polymers00
Water28816
1
A: NS2B
B: NS3 protease


Theoretical massNumber of molelcules
Total (without water)24,3812
Polymers24,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-27 kcal/mol
Surface area9200 Å2
MethodPISA
2
H: NS3 protease
G: NS2B


Theoretical massNumber of molelcules
Total (without water)24,3812
Polymers24,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area9320 Å2
MethodPISA
3
E: NS2B
F: NS3 protease


Theoretical massNumber of molelcules
Total (without water)24,3812
Polymers24,3812
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-23 kcal/mol
Surface area9280 Å2
MethodPISA
4
C: NS2B
D: NS3 protease


Theoretical massNumber of molelcules
Total (without water)24,3812
Polymers24,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-26 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.019, 151.670, 60.255
Angle α, β, γ (deg.)90.000, 111.268, 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
NS2B


Mass: 6022.470 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S1IYJ2, UniProt: A0A1W6I1A1*PLUS
#2: Protein
NS3 protease


Mass: 18358.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A346G7J0, UniProt: A0A1W6I1A1*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8.5, 0.1 M LiCl and 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9866 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9866 Å / Relative weight: 1
ReflectionResolution: 2.9→29.2 Å / Num. obs: 22135 / % possible obs: 98 % / Redundancy: 6.5 % / Biso Wilson estimate: 82.74 Å2 / CC1/2: 0.32 / Net I/σ(I): 7.22
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 2232 / CC1/2: 0.32

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fom

2fom


Resolution: 2.9→29.2 Å / SU ML: 0.4792 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3922
RfactorNum. reflection% reflection
Rfree0.2683 1153 5.28 %
Rwork0.2523 --
obs0.2532 21822 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 98.18 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 0 16 5479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675574
X-RAY DIFFRACTIONf_angle_d1.03477603
X-RAY DIFFRACTIONf_chiral_restr0.0743860
X-RAY DIFFRACTIONf_plane_restr0.0059995
X-RAY DIFFRACTIONf_dihedral_angle_d20.68781803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.4239980.37252676X-RAY DIFFRACTION99.64
3.03-3.190.35951580.33632599X-RAY DIFFRACTION99.39
3.19-3.390.32911640.33052578X-RAY DIFFRACTION99.13
3.39-3.650.36461460.37932461X-RAY DIFFRACTION94.35
3.65-4.020.35861250.35412469X-RAY DIFFRACTION92.48
4.02-4.60.251830.21172574X-RAY DIFFRACTION99.75
4.6-5.790.23181490.19872625X-RAY DIFFRACTION99.86
5.79-29.70.17681300.17942687X-RAY DIFFRACTION99.82

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