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- PDB-5wz2: Crystal structure of Zika virus NS5 methyltransferase bound to SA... -

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Basic information

Entry
Database: PDB / ID: 5wz2
TitleCrystal structure of Zika virus NS5 methyltransferase bound to SAM and RNA analogue (m7GpppA)
ComponentsNS5 MTase
KeywordsTRANSFERASE / Zika virus / methytransferase / RNA analogue / SAM
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 / induction by virus of host autophagy / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / structural molecule activity / virion attachment to host cell / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / cytoplasm
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 non-structural protein NS2B ...: / 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 / 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
Chem-GTA / S-ADENOSYLMETHIONINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDuan, W. / Song, H. / Qi, J. / Shi, Y. / Gao, G.F.
CitationJournal: EMBO J. / Year: 2017
Title: The crystal structure of Zika virus NS5 reveals conserved drug targets.
Authors: Duan, W. / Song, H. / Wang, H. / Chai, Y. / Su, C. / Qi, J. / Shi, Y. / Gao, G.F.
History
DepositionJan 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: NS5 MTase
B: NS5 MTase
C: NS5 MTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6319
Polymers92,0733
Non-polymers3,5586
Water1,62190
1
A: NS5 MTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8773
Polymers30,6911
Non-polymers1,1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS5 MTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8773
Polymers30,6911
Non-polymers1,1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NS5 MTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8773
Polymers30,6911
Non-polymers1,1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.131, 78.274, 136.380
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NS5 MTase / Genome polyprotein


Mass: 30691.004 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 2525-2794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A140E7U5, UniProt: A0A109PRQ3*PLUS
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H22N6O5S
#3: Chemical ChemComp-GTA / P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / 7-METHYL-GPPPA


Mass: 787.441 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C21H30N10O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24447 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.161 / Net I/σ(I): 9.362
Reflection shellResolution: 2.6→2.69 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9K
Resolution: 2.6→42.456 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.2468 1205 5.07 %
Rwork0.2024 --
obs0.2048 23751 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 234 90 6387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046438
X-RAY DIFFRACTIONf_angle_d0.9138724
X-RAY DIFFRACTIONf_dihedral_angle_d15.8142439
X-RAY DIFFRACTIONf_chiral_restr0.034936
X-RAY DIFFRACTIONf_plane_restr0.0041077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5964-2.70030.3125870.26251971X-RAY DIFFRACTION76
2.7003-2.82320.35571190.26172447X-RAY DIFFRACTION95
2.8232-2.9720.31971320.25822553X-RAY DIFFRACTION99
2.972-3.15820.29351330.24432606X-RAY DIFFRACTION100
3.1582-3.40190.28861500.22262587X-RAY DIFFRACTION100
3.4019-3.74410.28741370.19492556X-RAY DIFFRACTION100
3.7441-4.28540.20661610.17252560X-RAY DIFFRACTION100
4.2854-5.39740.18541570.16782605X-RAY DIFFRACTION100
5.3974-42.46160.22321290.19282661X-RAY DIFFRACTION100
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6136-0.11620.05120.6416-0.10280.571-0.0501-0.02460.03980.04030.0262-0.0573-0.0143-0.04740.1048-0.0054-0.0130.1463-0.01580.13321.06634.549711.5344
20.37390.2913-0.14380.69250.05240.84970.05130.0013-0.03450.022-0.02860.00040.0314-0.06750.2119-0.0079-0.02150.2528-0.01130.207224.346437.772932.89
30.4693-0.709-0.27551.08750.51380.65250.02570.02460.0652-0.05460.0081-0.1043-0.0122-0.01660.3108-0.02190.03680.2746-0.01720.292422.3169-0.458557.5397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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