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- PDB-5tmh: Structure of Zika virus NS5 -

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Basic information

Entry
Database: PDB / ID: 5tmh
TitleStructure of Zika virus NS5
ComponentsPolyproteinProteolysis
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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 ...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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 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 / virus-mediated perturbation of host defense response / 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 / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / 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 envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / 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 envelope glycoprotein E, stem/anchor domain / 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. / 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 / Vaccinia Virus protein VP39 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.278 Å
AuthorsWang, B. / Tan, X. / Song, J.
CitationJournal: Nat Commun / Year: 2017
Title: The structure of Zika virus NS5 reveals a conserved domain conformation.
Authors: Wang, B. / Tan, X.F. / Thurmond, S. / Zhang, Z.M. / Lin, A. / Hai, R. / Song, J.
History
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Polyprotein
B: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,60214
Polymers206,0112
Non-polymers1,59112
Water0
1
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8017
Polymers103,0061
Non-polymers7956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8017
Polymers103,0061
Non-polymers7956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.136, 136.478, 196.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Polyprotein / Proteolysis


Mass: 103005.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: A0A192GPS6, UniProt: Q32ZE1*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H8O3

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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: 3.12 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.7-0.9 M lithium sulfate, 0.1 M MES, pH 6-7

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.278→50 Å / Num. obs: 39593 / % possible obs: 99.4 % / Redundancy: 6.2 % / Net I/σ(I): 5.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.278→49.244 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2933 1987 5.04 %
Rwork0.262 --
obs0.2636 39406 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.278→49.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13339 0 90 0 13429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213741
X-RAY DIFFRACTIONf_angle_d0.54318691
X-RAY DIFFRACTIONf_dihedral_angle_d16.0968024
X-RAY DIFFRACTIONf_chiral_restr0.0392039
X-RAY DIFFRACTIONf_plane_restr0.0042399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2785-3.36040.39691170.35722248X-RAY DIFFRACTION84
3.3604-3.45130.35731390.32742612X-RAY DIFFRACTION98
3.4513-3.55280.36981420.31192659X-RAY DIFFRACTION99
3.5528-3.66750.35191410.30222640X-RAY DIFFRACTION99
3.6675-3.79850.29871420.27862684X-RAY DIFFRACTION99
3.7985-3.95050.2851420.27432666X-RAY DIFFRACTION99
3.9505-4.13020.32581430.26032698X-RAY DIFFRACTION100
4.1302-4.34780.26741400.23722655X-RAY DIFFRACTION100
4.3478-4.62010.25061440.23232705X-RAY DIFFRACTION100
4.6201-4.97650.28491430.23232712X-RAY DIFFRACTION100
4.9765-5.47670.27271450.24682735X-RAY DIFFRACTION100
5.4767-6.26780.31391460.26072727X-RAY DIFFRACTION100
6.2678-7.89150.25751490.24892789X-RAY DIFFRACTION100
7.8915-49.250.23731540.22252889X-RAY DIFFRACTION99
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)
14.14810.57030.15660.6491-0.10570.26050.2373-0.38830.29420.0078-0.0655-0.0695-0.2215-0.0352-0.16830.49020.11120.06320.8625-0.10550.497685.6036106.581466.9687
21.69630.5608-0.32250.26430.0670.81370.2018-0.5958-0.31640.12020.0325-00.16880.5894-0.22410.50040.1355-0.02870.53810.06060.597178.587594.497765.9064
30.94650.1638-0.3420.117-0.24050.83420.08510.0344-0.04610.03470.01910.0395-0.04210.1011-0.09690.38050.10530.02280.18880.0330.384345.2235109.712549.6749
42.05140.08190.22653.05890.70531.41920.13840.56820.872-0.1836-0.4025-0.2648-0.47620.18980.2720.590.14350.07990.57650.26210.693161.7485129.37228.06
53.075-0.4681-0.72631.16580.41560.79950.0649-0.47540.0593-0.03330.0794-0.0702-0.2055-0.2151-0.17960.46160.1577-0.02821.02920.03170.39955.6703106.7792100.3956
61.6065-0.00030.47380.5670.43990.420.0820.3353-0.0365-0.0651-0.0309-0.1654-0.05710.032-0.03560.42830.20510.03481.3040.09360.412596.8905103.1858113.6719
71.03230.06450.28970.6868-0.26922.40690.23320.57270.24140.1014-0.18-0.3566-0.51120.254-0.07830.60480.16580.06730.99740.11390.713489.802125.2734134.5615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 218 )
2X-RAY DIFFRACTION2chain 'A' and (resid 219 through 288 )
3X-RAY DIFFRACTION3chain 'A' and (resid 289 through 834 )
4X-RAY DIFFRACTION4chain 'A' and (resid 835 through 887 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 244 )
6X-RAY DIFFRACTION6chain 'B' and (resid 245 through 695 )
7X-RAY DIFFRACTION7chain 'B' and (resid 696 through 887 )

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