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- PDB-9yhi: Crystal structure of Chikungunya virus nsP3 macrodomain N24A muta... -

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Basic information

Entry
Database: PDB / ID: 9yhi
TitleCrystal structure of Chikungunya virus nsP3 macrodomain N24A 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'-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
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 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)74,61711
Polymers74,3684
Non-polymers2487
Water13,115728
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6282
Polymers18,5921
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6633
Polymers18,5921
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6633
Polymers18,5921
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6633
Polymers18,5921
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.816, 87.816, 85.552
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: 18592.098 Da / Num. of mol.: 4 / Fragment: macrodomain / Mutation: N24A
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
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: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11582 Å / Relative weight: 1
ReflectionResolution: 1.43→43.91 Å / Num. obs: 136366 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Χ2: 0.93 / Net I/σ(I): 14.8 / Num. measured all: 678429
Reflection shellResolution: 1.43→1.45 Å / % possible obs: 99.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.657 / Num. measured all: 32738 / Num. unique obs: 6761 / CC1/2: 0.32 / Rpim(I) all: 0.839 / Rrim(I) all: 1.86 / Χ2: 0.68 / Net I/σ(I) obs: 0.8

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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: 1.43→39.06 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 15.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 7013 5.15 %
Rwork0.1355 --
obs0.1377 136292 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 7 728 5653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075172
X-RAY DIFFRACTIONf_angle_d0.8377032
X-RAY DIFFRACTIONf_dihedral_angle_d12.8511941
X-RAY DIFFRACTIONf_chiral_restr0.072781
X-RAY DIFFRACTIONf_plane_restr0.009926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.31682080.29574314X-RAY DIFFRACTION99
1.45-1.460.30422340.27194347X-RAY DIFFRACTION100
1.46-1.480.2532280.25184288X-RAY DIFFRACTION100
1.48-1.50.28342050.23294349X-RAY DIFFRACTION100
1.5-1.520.25192210.22154307X-RAY DIFFRACTION100
1.52-1.540.25252240.21314333X-RAY DIFFRACTION100
1.54-1.560.26962620.20694247X-RAY DIFFRACTION100
1.56-1.590.24232140.18164411X-RAY DIFFRACTION100
1.59-1.610.23742420.16194256X-RAY DIFFRACTION100
1.61-1.640.221820.1534355X-RAY DIFFRACTION100
1.64-1.670.20352260.14554313X-RAY DIFFRACTION100
1.67-1.70.1872450.14224354X-RAY DIFFRACTION100
1.7-1.730.18722180.13554336X-RAY DIFFRACTION100
1.73-1.760.18672260.12794275X-RAY DIFFRACTION100
1.76-1.80.1891910.12084344X-RAY DIFFRACTION100
1.8-1.840.15672220.11824310X-RAY DIFFRACTION100
1.84-1.890.16482880.11224250X-RAY DIFFRACTION100
1.89-1.940.20142540.12684348X-RAY DIFFRACTION100
1.94-20.17312400.11534284X-RAY DIFFRACTION100
2-2.060.18272110.11214317X-RAY DIFFRACTION100
2.06-2.140.17622560.11064294X-RAY DIFFRACTION100
2.14-2.220.1642390.11244295X-RAY DIFFRACTION100
2.22-2.320.16282730.12494304X-RAY DIFFRACTION100
2.32-2.450.17392630.11914285X-RAY DIFFRACTION100
2.45-2.60.15032340.12644313X-RAY DIFFRACTION100
2.6-2.80.1922120.13534306X-RAY DIFFRACTION100
2.8-3.080.17781900.13774334X-RAY DIFFRACTION100
3.08-3.530.17782870.14234265X-RAY DIFFRACTION100
3.53-4.440.1522450.12454272X-RAY DIFFRACTION100
4.44-39.060.16142730.13794273X-RAY DIFFRACTION100

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