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- PDB-3gpg: Crystal structure of macro domain of Chikungunya virus -

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Basic information

Entry
Database: PDB / ID: 3gpg
TitleCrystal structure of macro domain of Chikungunya virus
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / macro domain / X domain / Chikungunya / alphavirus / virus / VIZIER. Viral enzymes involved in replication / ATP-binding / Cell membrane / Endosome / Helicase / Hydrolase / Lipoprotein / Lysosome / Membrane / Methyltransferase / mRNA capping / mRNA processing / Multifunctional enzyme / Nucleotide-binding / Nucleotidyltransferase / Nucleus / Palmitate / Phosphoprotein / Protease / RNA replication / RNA-binding / RNA-directed RNA polymerase / Thiol protease / Transferase
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 / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...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 / 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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase ...: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.65 Å
AuthorsMalet, H. / Jamal, S. / Coutard, B. / Canard, B.
CitationJournal: J.Virol. / Year: 2009
Title: The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket
Authors: Malet, H. / Coutard, B. / Jamal, S. / Dutartre, H. / Papageorgiou, N. / Neuvonen, M. / Ahola, T. / Forrester, N. / Gould, E.A. / Lafitte, D. / Ferron, F. / Lescar, J. / Gorbalenya, A.E. / de ...Authors: Malet, H. / Coutard, B. / Jamal, S. / Dutartre, H. / Papageorgiou, N. / Neuvonen, M. / Ahola, T. / Forrester, N. / Gould, E.A. / Lafitte, D. / Ferron, F. / Lescar, J. / Gorbalenya, A.E. / de Lamballerie, X. / Canard, B.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)74,5404
Polymers74,5404
Non-polymers00
Water11,007611
1
A: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,6351
Polymers18,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,6351
Polymers18,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,6351
Polymers18,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,6351
Polymers18,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.061, 87.061, 84.492
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: 18635.123 Da / Num. of mol.: 4 / Fragment: sequence database residues 1334-1493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: Ross / Gene: nsP3 / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q8JUX6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 46% PEG 600, 100 mM hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionRedundancy: 31.1 % / Av σ(I) over netI: 5 / Number: 2000862 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / D res high: 1.8 Å / D res low: 84.819 Å / Num. obs: 64424 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6984.8299.410.0640.06432
4.025.6999.910.0630.06329.3
3.294.0299.810.0690.06930.9
2.853.2999.610.0710.07131.3
2.552.8599.210.0870.08731.6
2.322.5599.110.1080.10831.7
2.152.3298.910.1390.13931.8
2.012.1598.710.1920.19231.9
1.92.0198.210.3340.33431.9
1.81.987.310.5020.50228.1
ReflectionResolution: 1.65→35 Å / Num. obs: 86209 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.2 / Num. unique all: 12610 / Rsym value: 0.468 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→34.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.899 / SU B: 3.443 / SU ML: 0.053 / SU R Cruickshank DPI: 0.086 / SU Rfree: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4316 5 %RANDOM
Rwork0.166 ---
obs0.167 86176 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.51 Å2 / Biso mean: 16.449 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 0 611 5565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225097
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9576933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11423.744211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79815861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1241535
X-RAY DIFFRACTIONr_chiral_restr0.0860.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213871
X-RAY DIFFRACTIONr_mcbond_it0.6791.53258
X-RAY DIFFRACTIONr_mcangle_it1.22225273
X-RAY DIFFRACTIONr_scbond_it2.20431839
X-RAY DIFFRACTIONr_scangle_it3.4964.51647
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 309 -
Rwork0.269 6084 -
all-6393 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.26191.08841.3742.0554-1.21872.43350.1315-0.1853-0.01190.27540.31020.3437-0.0223-0.6387-0.44180.1391-0.0328-0.00470.34070.08610.128927.7727-33.64391.1226
20.5507-0.14450.15851.4051-0.88711.7686-0.06790.11-0.00170.10560.13480.0524-0.0392-0.1925-0.06690.04150.0439-0.00330.1495-0.00560.023336.2374-25.8788-8.3751
37.99751.21264.92846.0951-1.94878.38170.09680.0664-0.4547-0.01060.23740.11480.5892-0.3787-0.33420.153-0.02690.01180.1234-0.05040.133833.8771-43.6719-4.6459
41.8134-0.2444-2.01111.7174-0.953112.2485-0.1807-0.2997-0.11980.24240.0774-0.03040.59230.44240.10330.13860.0233-0.01680.10770.01520.111614.0985-4.87142.4838
51.15290.09330.55381.2988-0.34781.215-0.00940.03520.0623-0.0205-0.03550.0423-0.00230.02840.04490.0476-0.0076-0.00770.02640.0020.04675.1833-6.6567-14.2785
65.05731.818-1.4984.97422.62999.30780.1515-0.04730.3560.0782-0.0762-0.4265-0.28490.2777-0.07540.0537-0.046-0.01310.09690.06480.222620.88380.4727-11.5633
72.0476-0.73470.33784.3273-1.0615.52860.2049-0.1662-0.06370.34070.0540.3867-0.0027-0.405-0.2590.12530.01120.09490.05810.05140.1101-5.1608-42.46078.5385
80.65450.74710.04942.9327-0.720.9045-0.0013-0.0066-0.04970.1148-0.01-0.1363-0.06460.02510.01130.06390.01980.01450.0130.01840.08396.5624-38.37070.4613
910.167-0.46035.27246.68111.33159.9243-0.0674-0.42710.39530.52290.00440.3517-0.6405-0.25110.0630.20830.03110.12350.0366-0.00430.1111-5.038-29.48911.0313
104.7944-0.93352.902811.59252.47677.74660.09720.49390.2365-0.8785-0.49690.8235-0.1223-0.23070.39970.11370.1044-0.00970.35040.0360.1394-25.4783-36.9998-28.1835
113.726-1.57140.10430.95680.22590.49380.09990.2531-0.0488-0.0712-0.14970.0287-0.0312-0.0850.04980.0440.0540.03280.1170.00310.0563-19.9827-40.9208-15.9967
129.79156.56971.863415.86384.35778.53750.29970.70290.0073-0.6746-0.4207-0.676-0.11640.20540.12110.11560.12770.06710.35370.09820.0591-17.5995-37.066-32.8824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 16
2X-RAY DIFFRACTION2A17 - 143
3X-RAY DIFFRACTION3A144 - 160
4X-RAY DIFFRACTION4B-1 - 5
5X-RAY DIFFRACTION5B6 - 143
6X-RAY DIFFRACTION6B144 - 160
7X-RAY DIFFRACTION7C-1 - 16
8X-RAY DIFFRACTION8C17 - 142
9X-RAY DIFFRACTION9C143 - 159
10X-RAY DIFFRACTION10D1 - 10
11X-RAY DIFFRACTION11D11 - 143
12X-RAY DIFFRACTION12D144 - 159

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