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Entry
Database: PDB / ID: 7h9d
TitleGroup deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z728187792 (CHIKV_MacB-x1423)
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / Diamond Light Source / I04-1 / READDI / Chikungunya Virus / crystallographic fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA modification / regulation of cytoskeleton organization ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / 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 / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 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 / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / : / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / 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 / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / 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
4-(1H-imidazol-2-yl)pyridine / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
Chikungunya Virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsAschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. ...Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171292 United States
CitationJournal: To Be Published
Title: Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain
Authors: Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / ...Authors: Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F.
History
DepositionApr 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: 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)73,32132
Polymers71,2774
Non-polymers2,04428
Water10,791599
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,67313
Polymers17,8191
Non-polymers85412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2828
Polymers17,8191
Non-polymers4637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1995
Polymers17,8191
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1676
Polymers17,8191
Non-polymers3485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.680, 87.680, 85.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Non-structural protein 3 / nsP3


Mass: 17819.215 Da / Num. of mol.: 4 / Fragment: macrodomain
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

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Non-polymers , 5 types, 627 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C2H6OS / Source: (gene. exp.) Chikungunya Virus / Production host: Escherichia coli (E. coli) / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H12NO3 / Source: (gene. exp.) Chikungunya Virus / Production host: Escherichia coli (E. coli) / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Cl / Source: (gene. exp.) Chikungunya Virus / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-4FL / 4-(1H-imidazol-2-yl)pyridine


Mass: 145.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.53→56.81 Å / Num. obs: 111118 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.035 / Rrim(I) all: 0.114 / Χ2: 0.37 / Net I/σ(I): 9.2 / Num. measured all: 1144236
Reflection shellResolution: 1.53→1.56 Å / % possible obs: 100 % / Redundancy: 8.3 % / Rmerge(I) obs: 3.017 / Num. measured all: 45313 / Num. unique obs: 5459 / CC1/2: 0.317 / Rpim(I) all: 1.11 / Rrim(I) all: 3.221 / Χ2: 0.06 / Net I/σ(I) obs: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→56.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.451 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23729 5299 5.1 %RANDOM
Rwork0.20016 ---
obs0.20198 98136 93.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.832 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.21 Å20 Å2
2--0.41 Å20 Å2
3----1.33 Å2
Refinement stepCycle: 1 / Resolution: 1.53→56.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 106 599 5667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0148758
X-RAY DIFFRACTIONr_bond_other_d0.0010.0146742
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.6619474
X-RAY DIFFRACTIONr_angle_other_deg1.3021.59415596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51720.514350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.958151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5471569
X-RAY DIFFRACTIONr_chiral_restr0.0740.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021588
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8963.1884659
X-RAY DIFFRACTIONr_mcbond_other1.8953.1884660
X-RAY DIFFRACTIONr_mcangle_it3.0444.4874496
X-RAY DIFFRACTIONr_mcangle_other3.0454.4874495
X-RAY DIFFRACTIONr_scbond_it2.9733.6854099
X-RAY DIFFRACTIONr_scbond_other2.9743.6834096
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8395.1434979
X-RAY DIFFRACTIONr_long_range_B_refined8.46336.2367964
X-RAY DIFFRACTIONr_long_range_B_other8.46336.2417965
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.524 133 -
Rwork0.469 2478 -
obs--31.9 %

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