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- PDB-4o6b: Dengue Type2 Virus Non-structural protein 1 (NS1) Form 1 crystal -

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Basic information

Entry
Database: PDB / ID: 4o6b
TitleDengue Type2 Virus Non-structural protein 1 (NS1) Form 1 crystal
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / flavivirus / non-structural protein 1 / NS1
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / structural molecule activity / virion attachment to host cell / virion membrane / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.0005 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 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7914
Polymers85,3482
Non-polymers4422
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-17 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.879, 175.879, 81.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 42674.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Strain: Thailand/16681/1984 / Gene: NS1 / Plasmid: pH-Op64-7 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P29990
#2: 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: isolated from a genetically manipulated source
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 21% PEG 3350, 250 mM ammonium formate pH 6.6, 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: 0.97934 Å
DetectorType: MARMOSAIC 300 / Detector: CCD / Date: Aug 14, 2013 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.51
ReflectionResolution: 3→50 Å / Num. all: 19002 / Num. obs: 17731 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 73.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.8
Reflection shellResolution: 3→3.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2893 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O6D

4o6d


Resolution: 3.0005→47.006 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.37 / Phase error: 25.37 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1836 10.36 %Random
Rwork0.1847 ---
obs0.1922 17724 94.23 %-
all-19002 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.66 Å2 / Biso mean: 88.5512 Å2 / Biso min: 38.59 Å2
Refinement stepCycle: LAST / Resolution: 3.0005→47.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 28 0 5126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045257
X-RAY DIFFRACTIONf_angle_d0.7127127
X-RAY DIFFRACTIONf_chiral_restr0.046774
X-RAY DIFFRACTIONf_plane_restr0.002903
X-RAY DIFFRACTIONf_dihedral_angle_d12.1021938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0005-3.08160.31751400.31371235137583
3.0816-3.17220.33181400.27671252139287
3.1722-3.27460.26731390.25561235137487
3.2746-3.39160.28111420.25011308145088
3.3916-3.52730.26441420.24161243138586
3.5273-3.68780.35311170.33091053117074
3.6878-3.88220.2411210.21861139126079
3.8822-4.12530.21391380.17461223136184
4.1253-4.44360.1971330.15721227136086
4.4436-4.89030.14991350.14711274140987
4.8903-5.5970.16881440.15161244138887
5.597-7.04780.2081390.15181259139887
7.0478-47.01190.20241430.15071259140287
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)
14.58061.5963-0.97923.8425-2.51141.66080.3643-0.36570.23520.10930.32870.1174-1.03180.4446-0.00281.0478-0.4173-0.00380.1113-0.13640.8563-4.0947-16.2444-22.1177
24.31980.9110.47439.07651.45535.96880.2465-0.68660.3523-0.012-0.06711.154-0.9701-0.791-0.09120.60420.17290.0310.7171-0.15290.6157-29.5535-21.6114-3.4427
35.2769-1.5176-2.9222.33260.67823.39860.02720.04150.1960.1453-0.06040.27810.2938-1.3350.17160.7015-0.28360.07160.8156-0.08140.5575-27.2796-28.1855-4.3907
44.2054-1.0151-2.67342.09621.0254.977-0.2928-0.31070.0553-0.0920.3506-0.0220.92240.1006-0.0390.6609-0.056-0.16030.27210.04210.5368-6.2285-34.7666-18.7159
53.85320.31330.83330.9414-0.40123.65730.0227-0.4055-0.12350.3147-0.0984-0.39670.88961.18670.06741.04810.2565-0.13960.7174-0.01630.53465.0902-40.639-1.6196
64.69140.25421.93983.03832.90784.2082-0.23150.19651.0823-0.365-0.22670.7485-1.90390.47810.17441.104-0.48130.09970.5456-0.00671.0689-6.6065-14.9323-32.0921
72.89773.8029-0.67015.32050.13988.17870.23130.3062-0.80850.1329-0.6311-0.8042-0.10692.44150.21160.46750.1361-0.18441.45370.03921.188616.5233-35.4739-48.5575
85.1638-4.5649-1.26914.42412.6086.63780.2921-0.7880.0164-0.74480.5071-0.6805-0.44370.8956-0.39580.6424-0.1355-0.07191.03520.24330.842612.4832-31.8409-53.7997
93.4287-1.74380.71043.54011.65661.67190.29960.76670.9230.2105-0.6255-1.37380.63921.44310.35650.68070.1748-0.0161.29940.33760.77910.6976-38.5548-56.2173
107.04260.13050.48895.4581-0.14776.37690.4170.38740.08740.182-0.3116-0.08670.54920.5284-0.28690.51040.12190.08090.6819-0.08360.54947.4542-36.0276-45.678
110.3574-0.3636-0.07072.59850.23120.61640.17260.15380.0374-0.13610.2320.1696-0.13320.06150.39260.7402-0.2815-0.15490.18730.02910.7154-8.4987-27.4109-31.6552
121.82860.0679-0.12092.2456-0.56645.2939-0.033-0.12390.025-0.06910.06870.21930.24820.03890.15110.5313-0.116-0.08280.2864-0.01580.4527-11.9734-32.3032-37.236
130.20230.22810.53730.25760.6051.4494-0.18290.1040.08860.01870.2678-0.37811.0378-0.71110.00680.8601-0.29860.02670.38940.00730.6714-15.0767-38.5709-39.2806
146.67960.6455-0.2642.86910.32452.86060.28391.0753-0.1589-0.17150.03690.6310.4216-1.1397-0.33190.6083-0.0686-0.21640.74350.0050.6013-23.4816-31.7645-49.4165
154.3354-1.43490.45451.28760.39913.22670.2710.42560.2952-0.1621-0.19180.25160.5262-1.1117-0.08060.6806-0.3982-0.09951.04510.15220.5984-25.7549-32.0672-56.092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 33 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 81 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 180 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 257 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 349 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 31 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 52 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 81 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 135 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 180 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 181 through 196 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 197 through 237 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 238 through 257 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 258 through 292 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 293 through 349 )B0

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