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- PDB-6w8y: Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone f... -

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Basic information

Entry
Database: PDB / ID: 6w8y
TitleCo-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments
ComponentsNonstructural polyprotein
KeywordsVIRAL PROTEIN / nsP3 / Macrodomain / pyrimidone fragments
Function / homology
Function and homology information


ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / regulation of cytoskeleton organization ...ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / GTP binding / host cell nucleus / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
: / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase ...: / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral superfamily 1 RNA helicase core domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2-oxo-2,3-dihydropyrimidine-4-carboxylic acid / Polyprotein P1234 / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsZhang, S. / Garzan, A. / Pathak, A.K. / Augelli-Szafran, C.E. / Wu, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI142759-01 United States
CitationJournal: Plos One / Year: 2021
Title: Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design.
Authors: Zhang, S. / Garzan, A. / Haese, N. / Bostwick, R. / Martinez-Gzegozewska, Y. / Rasmussen, L. / Streblow, D.N. / Haise, M.T. / Pathak, A.K. / Augelli-Szafran, C.E. / Wu, M.
History
DepositionMar 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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: Nonstructural polyprotein
B: Nonstructural polyprotein
C: Nonstructural polyprotein
D: Nonstructural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6368
Polymers74,0764
Non-polymers5604
Water1,72996
1
A: Nonstructural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,5191
Non-polymers1401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nonstructural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,5191
Non-polymers1401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nonstructural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,5191
Non-polymers1401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nonstructural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,5191
Non-polymers1401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.427, 87.427, 83.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Nonstructural polyprotein


Mass: 18518.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta pLysS / References: UniProt: A0A4D6GPC4, UniProt: Q8JUX6*PLUS
#2: Chemical
ChemComp-TJJ / 2-oxo-2,3-dihydropyrimidine-4-carboxylic acid


Mass: 140.097 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 21-24% PEG 400, 0.1 M sodium citrate pH5.6, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→75.71 Å / Num. obs: 41833 / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.145 Å / Rmerge(I) obs: 0.499 / Num. unique obs: 2929

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UVQ

6uvq


Resolution: 2.1→75.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.283 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.194
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 2096 5 %RANDOM
Rwork0.2084 ---
obs0.2108 39585 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 175.35 Å2 / Biso mean: 58.77 Å2 / Biso min: 32.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å2-0 Å2
2---0.11 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 2.1→75.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 40 96 5064
Biso mean--56.86 60.87 -
Num. residues----642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135006
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174580
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6596786
X-RAY DIFFRACTIONr_angle_other_deg1.3191.58210604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58321.92250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.215814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7611536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021034
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 132 -
Rwork0.276 2929 -
all-3061 -
obs--99.32 %

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