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- PDB-4o6d: West Nile Virus Non-structural protein 1 (NS1) Form 1 crystal -

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Basic information

Entry
Database: PDB / ID: 4o6d
TitleWest Nile Virus Non-structural protein 1 (NS1) Form 1 crystal
Components(NS1) x 2
KeywordsVIRAL PROTEIN / flavivirus / non-structural protein 1 / NS1
Function / homology
Function and homology information


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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor 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. / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesWest Nile virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5936 Å
AuthorsAkey, D.L. / Smith, J.L.
CitationJournal: Science / Year: 2014
Title: Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system.
Authors: Akey, D.L. / Brown, W.C. / Dutta, S. / Konwerski, J. / Jose, J. / Jurkiw, T.J. / DelProposto, J. / Ogata, C.M. / Skiniotis, G. / Kuhn, R.J. / Smith, J.L.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS1
B: NS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,16813
Polymers84,9832
Non-polymers5,18511
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-16 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.689, 168.689, 92.894
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein NS1


Mass: 42612.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Strain: NY99 / Gene: NS1 / Plasmid: pH-Ac64-7 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: U3N977, UniProt: Q9Q6P4*PLUS
#2: Protein NS1


Mass: 42370.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Strain: NY99 / Gene: NS1 / Plasmid: pH-Ac64-7 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: U3N977, UniProt: Q9Q6P4*PLUS

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Sugars , 3 types, 5 molecules

#3: 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.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
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

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Non-polymers , 3 types, 219 molecules

#6: Chemical
ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100


Mass: 646.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 4.45 Å3/Da / Density % sol: 72.38 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3000, 5% Glycerol, 20 mM Sodium Citrate pH 5.5, vapor diffusion, sitting drop, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 / Detector: CCD / Date: Apr 11, 2013 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 47162 / Num. obs: 47838 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.2 % / Biso Wilson estimate: 83.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.1
Reflection shellResolution: 2.59→2.68 Å / Rmerge(I) obs: 1.558 / Mean I/σ(I) obs: 1.2 / % possible all: 94.8

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 33989
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
12.14-10064.90.619514
9.56-12.1459.80.808514
8.17-9.5662.70.831608
7.25-8.1765.10.825658
6.58-7.2561.80.837765
6.07-6.5863.10.868804
5.66-6.0763.90.878865
5.33-5.6661.70.885944
5.05-5.3364.90.888967
4.8-5.0567.60.9051024
4.59-4.867.40.921090
4.41-4.5982.50.911120
4.25-4.4190.10.9061170
4.1-4.25900.9051180
3.97-4.191.30.8941271
3.85-3.9790.10.8861271
3.74-3.8591.10.8761332
3.63-3.7490.50.891346
3.54-3.6390.20.8661409
3.45-3.5489.90.8621444
3.37-3.4589.20.8681457
3.3-3.3790.40.8481488
3.23-3.391.40.8571518
3.16-3.2389.30.8431578
3.1-3.1690.50.8231574
3.04-3.190.60.8251623
2.99-3.0489.90.7951664
2.9-2.9989.92791

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DM6.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5936→19.794 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.34 / σ(F): 1.07 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1911 2348 5 %
Rwork0.1625 --
obs0.1639 46980 99.37 %
all-47162 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.1776 Å2
Refinement stepCycle: LAST / Resolution: 2.5936→19.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5351 0 239 213 5803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085724
X-RAY DIFFRACTIONf_angle_d1.1157768
X-RAY DIFFRACTIONf_dihedral_angle_d15.1342142
X-RAY DIFFRACTIONf_chiral_restr0.068861
X-RAY DIFFRACTIONf_plane_restr0.004976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5936-2.64640.39421300.33592336X-RAY DIFFRACTION90
2.6464-2.70380.38441280.29792628X-RAY DIFFRACTION100
2.7038-2.76650.30131270.26012633X-RAY DIFFRACTION100
2.7665-2.83550.26591530.22932586X-RAY DIFFRACTION100
2.8355-2.9120.2961410.222642X-RAY DIFFRACTION100
2.912-2.99740.28661290.22392616X-RAY DIFFRACTION100
2.9974-3.09380.25271370.20312633X-RAY DIFFRACTION100
3.0938-3.20390.21781410.19272615X-RAY DIFFRACTION100
3.2039-3.33160.25881370.1892628X-RAY DIFFRACTION100
3.3316-3.48250.24921420.18052633X-RAY DIFFRACTION100
3.4825-3.6650.20311360.16982613X-RAY DIFFRACTION100
3.665-3.8930.18871380.1562657X-RAY DIFFRACTION100
3.893-4.19090.18831400.13872639X-RAY DIFFRACTION100
4.1909-4.60780.14041430.11762650X-RAY DIFFRACTION100
4.6078-5.26360.14611410.11852671X-RAY DIFFRACTION100
5.2636-6.59070.18771400.16962683X-RAY DIFFRACTION100
6.5907-19.79420.16061450.16472769X-RAY DIFFRACTION100
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)
11.2315-2.36470.0026.3080.37240.1895-0.2228-0.09250.47080.2560.1448-0.0525-0.25360.17880.0670.6026-0.1363-0.12840.7998-0.07270.545463.6467-52.926320.369
22.9114-0.87090.11297.2322-0.06422.6803-0.0074-0.12350.61710.80920.17211.1472-0.6953-0.9863-0.15190.45490.22710.05221.14410.03690.877935.6929-33.485521.1231
31.9777-1.3472-0.59526.015-0.06122.3977-0.1126-0.01050.25680.41610.16370.3434-0.192-0.74950.02440.3691-0.0721-0.06240.88360.00090.433745.8977-49.831318.7067
42.8470.5187-0.20152.5663-1.12432.7676-0.0983-0.049-0.12850.2110.3450.2690.5621-1.098-0.22420.5337-0.30060.00111.0773-0.00680.464739.0091-66.054525.9244
54.5682-2.6694-0.61772.2050.15154.1022-0.3216-0.2752-0.48810.46530.48040.68310.4048-1.0416-0.25480.6839-0.31220.01651.22470.11260.598234.1453-68.525334.1969
64.7401-3.624-0.68093.57482.48765.18750.01630.06480.3275-0.3646-0.1319-0.229-0.7926-0.05940.13250.6765-0.192-0.15280.7305-0.02820.569468.7006-57.346917.1158
74.2052-3.5386-0.30325.9851.7522.23910.18430.5377-0.6313-0.4391-0.05650.07540.6125-0.0261-0.11050.7181-0.2118-0.00440.6136-0.13570.526972.1629-80.34443.909
82.3427-0.94240.06844.0044-0.3474.7749-0.06720.76670.3165-0.9922-0.0453-0.1894-0.1518-0.04730.10030.7136-0.2632-0.01690.8630.05210.419761.929-57.1899-10.7044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 314 )
5X-RAY DIFFRACTION5chain 'A' and (resid 315 through 352 )
6X-RAY DIFFRACTION6chain 'B' and (resid -4 through 35 )
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 197 )
8X-RAY DIFFRACTION8chain 'B' and (resid 198 through 352 )

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