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- PDB-9yhl: Crystal structure of Chikungunya virus nsP3 macrodomain N24A D31N... -

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Basic information

Entry
Database: PDB / ID: 9yhl
TitleCrystal structure of Chikungunya virus nsP3 macrodomain N24A D31N 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
ADENOSINE-5-DIPHOSPHORIBOSE / Chem-AR6 / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 D31N 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)78,28011
Polymers74,3644
Non-polymers3,9157
Water11,890660
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7103
Polymers18,5911
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7103
Polymers18,5911
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7103
Polymers18,5911
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1502
Polymers18,5911
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.649, 87.649, 85.214
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: 18591.113 Da / Num. of mol.: 4 / Fragment: macrodomain / Mutation: N24A, D31N
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-APR / ADENOSINE-5-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 660 / 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: 51.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Lithium sulfate, 0.1 M Sodium HEPES pH 7.5, 25% (w/v) PEG3350

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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 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11582 Å / Relative weight: 1
ReflectionResolution: 1.51→43.82 Å / Num. obs: 114819 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.028 / Rrim(I) all: 0.063 / Χ2: 0.98 / Net I/σ(I): 15.4 / Num. measured all: 576734
Reflection shellResolution: 1.51→1.54 Å / % possible obs: 99.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 1.655 / Num. measured all: 25671 / Num. unique obs: 5604 / CC1/2: 0.292 / Rpim(I) all: 0.866 / Rrim(I) all: 1.873 / Χ2: 0.87 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata scaling
XDSJan 19, 2025 BUILT=20250430data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→43.82 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1851 5970 5.2 %
Rwork0.1327 --
obs0.1355 114770 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4938 0 252 660 5850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075568
X-RAY DIFFRACTIONf_angle_d1.0227617
X-RAY DIFFRACTIONf_dihedral_angle_d14.4292020
X-RAY DIFFRACTIONf_chiral_restr0.053840
X-RAY DIFFRACTIONf_plane_restr0.008964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.35541960.2913532X-RAY DIFFRACTION99
1.53-1.550.31731910.27363637X-RAY DIFFRACTION100
1.55-1.560.29442160.26263613X-RAY DIFFRACTION100
1.56-1.580.30581700.24493652X-RAY DIFFRACTION100
1.58-1.60.29031900.22433622X-RAY DIFFRACTION100
1.6-1.630.27481830.20643692X-RAY DIFFRACTION100
1.63-1.650.23661560.18943651X-RAY DIFFRACTION100
1.65-1.670.26842080.17793620X-RAY DIFFRACTION100
1.67-1.70.26532170.16643609X-RAY DIFFRACTION100
1.7-1.730.24831560.16523659X-RAY DIFFRACTION100
1.73-1.760.20852010.15073640X-RAY DIFFRACTION100
1.76-1.790.23971610.13673671X-RAY DIFFRACTION100
1.79-1.820.21231960.13433675X-RAY DIFFRACTION100
1.82-1.860.19732100.1283566X-RAY DIFFRACTION100
1.86-1.90.18732360.12113620X-RAY DIFFRACTION100
1.9-1.950.19322340.14443627X-RAY DIFFRACTION100
1.95-20.20931680.1293626X-RAY DIFFRACTION100
2-2.050.16771660.11233656X-RAY DIFFRACTION100
2.05-2.110.1852580.10783586X-RAY DIFFRACTION100
2.11-2.180.15361600.09873676X-RAY DIFFRACTION100
2.18-2.260.17012200.10943604X-RAY DIFFRACTION100
2.26-2.350.17142200.10873602X-RAY DIFFRACTION100
2.35-2.450.16072400.11523596X-RAY DIFFRACTION100
2.45-2.580.16411860.12283640X-RAY DIFFRACTION100
2.58-2.740.18722040.11713634X-RAY DIFFRACTION100
2.74-2.950.18131530.13563642X-RAY DIFFRACTION100
2.96-3.250.19271830.13663686X-RAY DIFFRACTION100
3.25-3.720.16682720.11913515X-RAY DIFFRACTION100
3.72-4.690.14462010.11273638X-RAY DIFFRACTION100
4.69-43.820.19062180.14763613X-RAY DIFFRACTION100

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