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- PDB-5u04: Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 5u04
TitleCrystal structure of Zika virus NS5 RNA-dependent RNA polymerase
ComponentsZika Virus NS5 RdRp
KeywordsVIRAL PROTEIN / NS5 / zika / virus / RNA / polymerase / drug
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 / 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 ...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 / 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 / membrane => GO:0016020 / 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 / 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 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
PHOSPHATE ION / Core protein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGodoy, A.S. / Lima, G.M.A. / Oliveira, K.I.Z. / Torres, N.U. / Maluf, F.V. / Guido, R.V.C. / Oliva, G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase.
Authors: Godoy, A.S. / Lima, G.M. / Oliveira, K.I. / Torres, N.U. / Maluf, F.V. / Guido, R.V. / Oliva, G.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
SupersessionMar 29, 2017ID: 5TIT
Revision 1.1Mar 29, 2017Group: Structure summary
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Apr 12, 2017Group: Database references
Revision 1.4Apr 26, 2017Group: Data collection
Revision 1.5Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Zika Virus NS5 RdRp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2454
Polymers69,0201
Non-polymers2263
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-46 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.954, 78.954, 210.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Zika Virus NS5 RdRp


Mass: 69019.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: H8XX10, UniProt: Q32ZE1*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate 1 M Sodium HEPES; 1 M MOPS (acid) 40% v/v Ethylene glycol; 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.47 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 1.9→29.66 Å / Num. obs: 53499 / % possible obs: 99.7 % / Redundancy: 24.3 % / CC1/2: 0.99 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.72 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.11rc2_2531: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hcn

2hcn


Resolution: 1.9→29.657 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 1999 3.76 %Random
Rwork0.1789 ---
obs0.18 53149 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 7 663 4525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063989
X-RAY DIFFRACTIONf_angle_d0.5755403
X-RAY DIFFRACTIONf_dihedral_angle_d5.893241
X-RAY DIFFRACTIONf_chiral_restr0.042574
X-RAY DIFFRACTIONf_plane_restr0.003686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.29231380.26463549X-RAY DIFFRACTION99
1.9475-2.00020.25841400.23423577X-RAY DIFFRACTION100
2.0002-2.0590.26931400.21763566X-RAY DIFFRACTION99
2.059-2.12540.22431400.19223611X-RAY DIFFRACTION100
2.1254-2.20140.24721410.17763607X-RAY DIFFRACTION100
2.2014-2.28950.19741410.17583603X-RAY DIFFRACTION100
2.2895-2.39360.22461430.17733635X-RAY DIFFRACTION100
2.3936-2.51980.19061410.17333618X-RAY DIFFRACTION100
2.5198-2.67760.1841420.1753631X-RAY DIFFRACTION100
2.6776-2.88410.22591430.1783655X-RAY DIFFRACTION100
2.8841-3.17410.20051440.17643688X-RAY DIFFRACTION100
3.1741-3.63270.17341440.15743690X-RAY DIFFRACTION100
3.6327-4.57410.17761470.15053755X-RAY DIFFRACTION100
4.5741-29.66020.22031550.19723965X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.5167 Å / Origin y: 71.7656 Å / Origin z: 104.8168 Å
111213212223313233
T0.0999 Å20.0027 Å2-0.0309 Å2-0.1525 Å20.0261 Å2--0.1575 Å2
L0.4815 °2-0.1049 °20.2406 °2-0.7314 °2-0.2958 °2--0.756 °2
S0.006 Å °0.0825 Å °-0.056 Å °0.0392 Å °-0.0503 Å °-0.1426 Å °0.0206 Å °0.165 Å °0.0241 Å °
Refinement TLS groupSelection details: all

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