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- PDB-5k6k: Zika virus non-structural protein 1 (NS1) -

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Basic information

Entry
Database: PDB / ID: 5k6k
TitleZika virus non-structural protein 1 (NS1)
ComponentsZika virus protein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase ...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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / GTP binding / 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsAkey, D.L. / Brown, W.C. / Smith, J.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Extended surface for membrane association in Zika virus NS1 structure.
Authors: Brown, W.C. / Akey, D.L. / Konwerski, J.R. / Tarrasch, J.T. / Skiniotis, G. / Kuhn, R.J. / Smith, J.L.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references / Structure summary
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Sep 21, 2016Group: Database references
Revision 1.4Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Zika virus protein
B: Zika virus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,28014
Polymers85,6382
Non-polymers1,64112
Water18,8621047
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-59 kcal/mol
Surface area31630 Å2
MethodPISA
2
A: Zika virus protein
B: Zika virus protein
hetero molecules

A: Zika virus protein
B: Zika virus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,56028
Polymers171,2774
Non-polymers3,28324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area18120 Å2
ΔGint-133 kcal/mol
Surface area60510 Å2
MethodPISA
3
A: Zika virus protein
B: Zika virus protein
hetero molecules

A: Zika virus protein
B: Zika virus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,56028
Polymers171,2774
Non-polymers3,28324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area17800 Å2
ΔGint-117 kcal/mol
Surface area60830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.160, 130.440, 147.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21A-950-

HOH

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Components

#1: Protein Zika virus protein /


Mass: 42819.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: unidentified baculovirus / References: UniProt: Q32ZE1
#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.: 4
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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1047 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 3350 150 mM NH3SO4 100 mM tris 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.89→48.08 Å / Num. obs: 74493 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 32.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.22
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.89-1.9213.31.6131.331100
1.92-1.961.4611.61100
1.96-21.1092.161100
2-2.040.9342.621100
2.04-2.080.7983.11100
2.08-2.130.6693.671100
2.13-2.180.5664.531100
2.18-2.240.5084.981100
2.24-2.310.4275.971100
2.31-2.380.357.211100
2.38-2.470.2918.541100
2.47-2.570.23910.11100
2.57-2.680.19712.31100
2.68-2.830.15614.931100
2.83-30.12419.041100
3-3.230.123.191100
3.23-3.560.07928.251100
3.56-4.080.06833.921100
4.08-5.130.06236.981100
5.130.0637.29199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.07 Å48.61 Å
Translation7.07 Å48.61 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O6D

4o6d


Resolution: 1.89→48.08 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.1889 2089 2.81 %
Rwork0.1486 --
obs0.1498 74473 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.22 Å2 / Biso mean: 38.6056 Å2 / Biso min: 15.11 Å2
Refinement stepCycle: final / Resolution: 1.89→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 99 1047 6770
Biso mean--80.31 51.33 -
Num. residues----704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075933
X-RAY DIFFRACTIONf_angle_d0.8388069
X-RAY DIFFRACTIONf_chiral_restr0.055850
X-RAY DIFFRACTIONf_plane_restr0.0051035
X-RAY DIFFRACTIONf_dihedral_angle_d18.0033539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8901-1.9340.35981360.30547694905
1.934-1.98240.31561400.255747634903
1.9824-2.0360.25491420.212947804922
2.036-2.09590.23591370.187247724909
2.0959-2.16360.23411340.174347814915
2.1636-2.24090.18391390.170448284967
2.2409-2.33060.18831390.169747794918
2.3306-2.43670.22761370.157947994936
2.4367-2.56510.20551380.153748024940
2.5651-2.72580.1891370.153248284965
2.7258-2.93630.1891410.146647994940
2.9363-3.23170.18261400.138148675007
3.2317-3.69920.17561420.129148524994
3.6992-4.660.15921410.112748935034
4.66-48.09550.16411460.145650725218
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)
12.81881.39070.39731.1370.00460.80990.0568-0.0841-0.26350.0821-0.0306-0.23430.02040.133-0.01990.21550.0236-0.03130.23110.0080.2535-3.2237-38.7751-14.1706
20.4647-0.3311-0.31122.10461.30832.0336-0.0044-0.06920.06850.00090.00250.0532-0.1672-0.0659-0.00060.1858-0.0099-0.01620.21590.02280.1965-27.1421-23.9272-11.8706
32.32460.27731.37542.56281.01644.29820.2611-0.2718-0.28380.1708-0.0963-0.14540.3299-0.3158-0.140.2462-0.0321-0.03280.18550.07080.2511-26.1711-55.0785-17.5835
42.96330.927-0.39272.5514-0.55911.72380.0845-0.2606-0.15450.1607-0.06780.25280.1387-0.106-0.01620.19-0.01720.00240.21180.02060.2252-56.8414-51.5902-31.0621
50.4988-0.1204-0.47831.05940.99213.629-0.0150.0514-0.0827-0.125-0.0131-0.04150.15190.13420.03380.22170.0008-0.0060.19040.02270.2229-26.294-51.0775-44.0288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 180 )A-5 - 180
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 352 )A181 - 352
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 31 )B0 - 31
4X-RAY DIFFRACTION4chain 'B' and (resid 32 through 180 )B32 - 180
5X-RAY DIFFRACTION5chain 'B' and (resid 181 through 352 )B181 - 352

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