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- PDB-9yhj: Crystal structure of Chikungunya virus nsP3 macrodomain N24A D31H... -

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Basic information

Entry
Database: PDB / ID: 9yhj
TitleCrystal structure of Chikungunya virus nsP3 macrodomain N24A D31H double mutant (P31 crystal form) in complex with ADP-ribose
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'-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 / 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
Chem-AR6 / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 N24A D31H double mutant (P31 crystal form) in complex with ADP-ribose
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)76,6988
Polymers74,4614
Non-polymers2,2374
Water3,981221
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1742
Polymers18,6151
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1742
Polymers18,6151
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1742
Polymers18,6151
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1742
Polymers18,6151
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.935, 87.935, 84.820
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: 18615.156 Da / Num. of mol.: 4 / Fragment: macrodomain / Mutation: N24A, 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-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium hydrogen citrate, 20% (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: Dec 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11582 Å / Relative weight: 1
ReflectionResolution: 1.86→43.97 Å / Num. obs: 61566 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Χ2: 0.94 / Net I/σ(I): 14.4 / Num. measured all: 313671
Reflection shellResolution: 1.86→1.9 Å / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 1.469 / Num. measured all: 19253 / Num. unique obs: 3770 / CC1/2: 0.375 / Rpim(I) all: 0.721 / Rrim(I) all: 1.639 / Χ2: 0.68 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSJan 19, 2025 BUILT=20250430data scaling
XDSJan 19, 2025 BUILT=20250430data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→43.97 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 3327 5.41 %
Rwork0.1423 --
obs0.1463 61524 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 144 221 5329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015241
X-RAY DIFFRACTIONf_angle_d1.0427132
X-RAY DIFFRACTIONf_dihedral_angle_d15.9231899
X-RAY DIFFRACTIONf_chiral_restr0.056797
X-RAY DIFFRACTIONf_plane_restr0.008898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.890.35781560.27242378X-RAY DIFFRACTION100
1.89-1.910.34271480.26012454X-RAY DIFFRACTION100
1.91-1.940.30831520.22862388X-RAY DIFFRACTION100
1.94-1.980.28921280.21632469X-RAY DIFFRACTION100
1.98-2.010.29821240.25272439X-RAY DIFFRACTION100
2.01-2.050.30681000.22872449X-RAY DIFFRACTION100
2.05-2.090.34231630.19212415X-RAY DIFFRACTION100
2.09-2.130.26421260.16822435X-RAY DIFFRACTION100
2.13-2.180.28131360.18342433X-RAY DIFFRACTION100
2.18-2.230.24981410.16332403X-RAY DIFFRACTION100
2.23-2.280.24711390.14942417X-RAY DIFFRACTION100
2.28-2.340.24791520.14642451X-RAY DIFFRACTION100
2.34-2.410.22751380.18082393X-RAY DIFFRACTION100
2.41-2.490.23581660.17442418X-RAY DIFFRACTION100
2.49-2.580.28151220.1662450X-RAY DIFFRACTION100
2.58-2.680.26041380.13372425X-RAY DIFFRACTION100
2.68-2.80.26191200.18122449X-RAY DIFFRACTION100
2.81-2.950.20331060.15782444X-RAY DIFFRACTION100
2.95-3.140.23411060.15452478X-RAY DIFFRACTION100
3.14-3.380.21561700.13142390X-RAY DIFFRACTION100
3.38-3.720.21161780.13552348X-RAY DIFFRACTION100
3.72-4.260.18971230.11292454X-RAY DIFFRACTION100
4.26-5.360.13561750.09472367X-RAY DIFFRACTION99
5.36-43.970.18361200.11332450X-RAY DIFFRACTION100

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