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- PDB-9zra: Crystal structure of macrodomain from Chikungunya virus -

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Basic information

Entry
Database: PDB / ID: 9zra
TitleCrystal structure of macrodomain from Chikungunya virus
ComponentsPolyprotein P1234
KeywordsVIRAL PROTEIN / MACRO DOMAIN / Chikungunya virus / alpha virus
Function / homology
Function and homology information


host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity ...host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / methylation / RNA helicase activity / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed RNA polymerase activity / host cell nucleus / GTP binding / host cell plasma membrane / proteolysis / DNA-templated transcription / RNA binding / ATP binding / metal ion binding
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 / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / 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: 1.3 Å
AuthorsChang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Crystal structure of macrodomain from Chikungunya virus
Authors: Chang, C. / Endre, M. / Stols, L. / Kim, Y. / Joachimiak, A.
History
DepositionDec 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyprotein P1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0344
Polymers17,8181
Non-polymers2163
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.031, 41.031, 103.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Polyprotein P1234 / Non-structural polyprotein


Mass: 17818.121 Da / Num. of mol.: 1 / Fragment: Macrodomain, residues 1334-1493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0U7D9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES PEG 8000 Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 42057 / % possible obs: 99.4 % / Redundancy: 10.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.027 / Rrim(I) all: 0.094 / Χ2: 0.991 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.3-1.323.10.43719200.8590.9610.240.5040.85490.8
1.32-1.354.10.46420240.8810.9680.2320.5230.87997.5
1.35-1.375.60.44221320.9220.9790.1960.4860.8799.8
1.37-1.47.50.43220770.9450.9860.1660.4630.976100
1.4-1.439.20.42621190.9630.9910.1480.4510.961100
1.43-1.4610.60.33821030.9820.9960.1090.3560.946100
1.46-1.510.80.27120980.9880.9970.0860.2850.968100
1.5-1.5410.90.23121200.9910.9980.0730.2430.935100
1.54-1.59110.19321300.9940.9980.0610.2030.948100
1.59-1.6411.10.16621020.9950.9990.0520.1740.88100
1.64-1.711.20.15621180.9950.9990.0490.1640.871100
1.7-1.7611.10.14721030.9960.9990.0450.1540.883100
1.76-1.8410.60.12921090.9970.9990.0410.1350.901100
1.84-1.9411.10.12621190.9970.9990.0390.1310.946100
1.94-2.0612.60.11421080.99810.0330.1191.042100
2.06-2.22130.1221170.9980.9990.0340.1251.1100
2.22-2.4513.50.13421410.99810.0380.1391.137100
2.45-2.813.60.11321080.99810.0320.1181.126100
2.8-3.5312.30.07321320.99810.0210.0761.147100
3.53-5013.50.05521770.99910.0160.0571.047100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→41.03 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 2019 5.12 %
Rwork0.1557 --
obs0.1572 39416 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 14 225 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051350
X-RAY DIFFRACTIONf_angle_d0.7531830
X-RAY DIFFRACTIONf_dihedral_angle_d12.094511
X-RAY DIFFRACTIONf_chiral_restr0.069200
X-RAY DIFFRACTIONf_plane_restr0.007241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.2189640.2219965X-RAY DIFFRACTION34
1.33-1.370.27721180.25432088X-RAY DIFFRACTION73
1.37-1.410.26321460.23652816X-RAY DIFFRACTION99
1.41-1.450.27981170.21322909X-RAY DIFFRACTION100
1.45-1.50.23631720.19682833X-RAY DIFFRACTION100
1.5-1.560.22511550.19272851X-RAY DIFFRACTION100
1.56-1.640.22481490.17592855X-RAY DIFFRACTION100
1.64-1.720.20681430.17532873X-RAY DIFFRACTION100
1.72-1.830.18981650.16032856X-RAY DIFFRACTION100
1.83-1.970.17031510.15452860X-RAY DIFFRACTION100
1.97-2.170.19751980.15212832X-RAY DIFFRACTION100
2.17-2.480.19171660.14942844X-RAY DIFFRACTION100
2.48-3.130.18441250.14832906X-RAY DIFFRACTION100
3.13-41.030.13861500.12742909X-RAY DIFFRACTION100

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