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- PDB-9yhc: Crystal structure of Chikungunya virus nsP3 macrodomain D31H muta... -

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Basic information

Entry
Database: PDB / ID: 9yhc
TitleCrystal structure of Chikungunya virus nsP3 macrodomain D31H mutant (P31 crystal form)
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / HYDROLASE / Chikungunya virus / ADP-ribose / AViDD / Advanced Light Source 8.3.1
Function / homology
Function and homology information


ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-phosphatase / mRNA 5'-triphosphate monophosphatase activity / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA modification / regulation of cytoskeleton organization ...ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-phosphatase / mRNA 5'-triphosphate monophosphatase activity / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / 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 / 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 / symbiont-mediated suppression of host innate immune response / RNA helicase / 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
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCorrey, G.J. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171110 United States
CitationJournal: To Be Published
Title: Crystal structure of Chikungunya virus nsP3 macrodomain D31H mutant (P31 crystal form)
Authors: Correy, G.J. / Fraser, J.S.
History
DepositionSep 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
C: Non-structural protein 3
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,56426
Polymers74,6334
Non-polymers93222
Water11,403633
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9388
Polymers18,6581
Non-polymers2797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8676
Polymers18,6581
Non-polymers2095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8676
Polymers18,6581
Non-polymers2095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8936
Polymers18,6581
Non-polymers2355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.445, 87.445, 85.293
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Non-structural protein 3 / nsP3


Mass: 18658.184 Da / Num. of mol.: 4 / Fragment: macrodomain / Mutation: D31H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q8JUX6, ADP-ribose 1''-phosphate phosphatase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium malonate dibasic monohydrate pH 7, 24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11582 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11582 Å / Relative weight: 1
ReflectionResolution: 1.35→43.72 Å / Num. obs: 159674 / % possible obs: 99.6 % / Redundancy: 4.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.071 / Rrim(I) all: 0.16 / Χ2: 0.64 / Net I/σ(I): 5.8 / Num. measured all: 784984
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 92.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 1.017 / Num. measured all: 27125 / Num. unique obs: 7343 / CC1/2: 0.48 / Rpim(I) all: 0.584 / Rrim(I) all: 1.179 / Χ2: 0.27 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSJan 19, 2025 BUILT=20250430data scaling
PHASERphasing
XDSJan 19, 2025 BUILT=20250430data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→38.91 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 13.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1718 8262 5.18 %
Rwork0.1356 --
obs0.1375 159572 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 37 633 5752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075392
X-RAY DIFFRACTIONf_angle_d0.8627318
X-RAY DIFFRACTIONf_dihedral_angle_d12.4992025
X-RAY DIFFRACTIONf_chiral_restr0.074797
X-RAY DIFFRACTIONf_plane_restr0.008962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.35112540.31644530X-RAY DIFFRACTION90
1.37-1.380.30472710.29054945X-RAY DIFFRACTION98
1.38-1.40.28122680.26145090X-RAY DIFFRACTION100
1.4-1.420.25042640.24195072X-RAY DIFFRACTION100
1.42-1.430.2313010.21465088X-RAY DIFFRACTION100
1.43-1.450.2332850.20835057X-RAY DIFFRACTION100
1.45-1.470.2262500.19895070X-RAY DIFFRACTION100
1.48-1.50.19832530.18285081X-RAY DIFFRACTION100
1.5-1.520.21092720.17715081X-RAY DIFFRACTION100
1.52-1.550.21682840.17345082X-RAY DIFFRACTION100
1.55-1.570.2072760.16345016X-RAY DIFFRACTION100
1.57-1.60.18662620.13885094X-RAY DIFFRACTION100
1.6-1.630.18262340.1265112X-RAY DIFFRACTION100
1.63-1.660.17772680.11625057X-RAY DIFFRACTION100
1.66-1.70.15082950.11715122X-RAY DIFFRACTION100
1.7-1.740.15912300.11485081X-RAY DIFFRACTION100
1.74-1.780.16712600.11145087X-RAY DIFFRACTION100
1.78-1.830.17192440.10845030X-RAY DIFFRACTION100
1.83-1.890.163280.10495033X-RAY DIFFRACTION100
1.89-1.950.16513280.10625030X-RAY DIFFRACTION100
1.95-2.020.16572340.10965099X-RAY DIFFRACTION100
2.02-2.10.16442980.10795037X-RAY DIFFRACTION100
2.1-2.190.15092570.11035105X-RAY DIFFRACTION100
2.19-2.310.17153390.11735005X-RAY DIFFRACTION100
2.31-2.450.15973000.12015019X-RAY DIFFRACTION100
2.45-2.640.14952640.12935067X-RAY DIFFRACTION100
2.64-2.910.1682610.13745117X-RAY DIFFRACTION100
2.91-3.330.17262500.14135053X-RAY DIFFRACTION100
3.33-4.190.16583230.13345020X-RAY DIFFRACTION100
4.2-38.910.1623090.14355030X-RAY DIFFRACTION100

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