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- PDB-5mrk: Structural basis of Zika virus methyltransferase inhibition by si... -

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Basic information

Entry
Database: PDB / ID: 5mrk
TitleStructural basis of Zika virus methyltransferase inhibition by sinefungin
Componentsmethyltransferase
KeywordsTRANSFERASE / zika / virus / methyltransferase / sinefungin
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 / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding ...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 / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / 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 / molecular adaptor activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / centrosome / 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 / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHercik, K. / Boura, E.
CitationJournal: Arch. Virol. / Year: 2017
Title: Structural basis of Zika virus methyltransferase inhibition by sinefungin.
Authors: Hercik, K. / Brynda, J. / Nencka, R. / Boura, E.
History
DepositionDec 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: methyltransferase
B: methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4576
Polymers58,6232
Non-polymers8344
Water5,891327
1
A: methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7283
Polymers29,3111
Non-polymers4172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7283
Polymers29,3111
Non-polymers4172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.840, 52.010, 84.170
Angle α, β, γ (deg.)90.00, 107.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein methyltransferase /


Mass: 29311.482 Da / Num. of mol.: 2 / Fragment: UNP residues 2521-2784
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: A0A1B0YUR2, UniProt: A0A024B7W1*PLUS
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM sodium acetate pH 4.6, 39% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.9→31.24 Å / Num. obs: 82986 / % possible obs: 98.67 % / Redundancy: 5.18 % / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.01
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 1.605 / Mean I/σ(I) obs: 0.7 / CC1/2: 0.382 / % possible all: 92.06

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KQR

5kqr


Resolution: 1.9→31.24 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 4141 4.99 %
Rwork0.2266 --
obs0.2287 82986 89.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 56 327 4297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054073
X-RAY DIFFRACTIONf_angle_d0.7255507
X-RAY DIFFRACTIONf_dihedral_angle_d15.8122420
X-RAY DIFFRACTIONf_chiral_restr0.044596
X-RAY DIFFRACTIONf_plane_restr0.005698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.69381040.57031855X-RAY DIFFRACTION63
1.9216-1.94420.82331080.69192053X-RAY DIFFRACTION72
1.9442-1.96790.5761180.55062248X-RAY DIFFRACTION76
1.9679-1.99280.36941140.35052174X-RAY DIFFRACTION74
1.9928-2.0190.38471200.3252317X-RAY DIFFRACTION78
2.019-2.04670.29331230.3122256X-RAY DIFFRACTION80
2.0467-2.07590.36691250.31422357X-RAY DIFFRACTION80
2.0759-2.10690.30741230.28452411X-RAY DIFFRACTION83
2.1069-2.13980.27221310.26332526X-RAY DIFFRACTION86
2.1398-2.17490.3081340.26292525X-RAY DIFFRACTION87
2.1749-2.21240.27491360.24872620X-RAY DIFFRACTION89
2.2124-2.25260.29581370.27362648X-RAY DIFFRACTION89
2.2526-2.29590.29181350.25462620X-RAY DIFFRACTION91
2.2959-2.34280.29391490.23962780X-RAY DIFFRACTION94
2.3428-2.39370.25041510.22612777X-RAY DIFFRACTION95
2.3937-2.44930.27951440.24132788X-RAY DIFFRACTION96
2.4493-2.51060.3041440.2222787X-RAY DIFFRACTION96
2.5106-2.57840.311480.2252875X-RAY DIFFRACTION96
2.5784-2.65420.28491450.23392802X-RAY DIFFRACTION96
2.6542-2.73990.27441490.21672838X-RAY DIFFRACTION96
2.7399-2.83770.2561450.21792814X-RAY DIFFRACTION97
2.8377-2.95130.29331460.23032811X-RAY DIFFRACTION97
2.9513-3.08550.2741490.22962837X-RAY DIFFRACTION97
3.0855-3.2480.30971460.21722810X-RAY DIFFRACTION96
3.248-3.45120.26041480.20862868X-RAY DIFFRACTION98
3.4512-3.71730.21681560.19272909X-RAY DIFFRACTION99
3.7173-4.09070.22451540.18342860X-RAY DIFFRACTION99
4.0907-4.68090.20591530.182921X-RAY DIFFRACTION99
4.6809-5.8910.20781570.18952905X-RAY DIFFRACTION100
5.891-31.24450.24881490.21442853X-RAY DIFFRACTION98

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