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- PDB-3gpo: Crystal structure of macro domain of Chikungunya virus in complex... -

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Basic information

Entry
Database: PDB / ID: 3gpo
TitleCrystal structure of macro domain of Chikungunya virus in complex with ADP-ribose
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / macro domain / X domain / Chikungunya / alphavirus / virus / VIZIER. Viral enzymes involved in replication / ADP-ribose / 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


ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / mRNA 5'-phosphatase / mRNA 5'-triphosphate monophosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA modification / regulation of cytoskeleton organization ...ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / mRNA 5'-phosphatase / mRNA 5'-triphosphate monophosphatase 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 / 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 / RNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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 / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / (+) 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)77,5288
Polymers75,2914
Non-polymers2,2374
Water8,773487
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3822
Polymers18,8231
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3822
Polymers18,8231
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3822
Polymers18,8231
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3822
Polymers18,8231
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.957, 87.957, 84.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Non-structural protein 3 / nsP3


Mass: 18822.703 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: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.74 %
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: ID23-1 / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. all: 57460 / Num. obs: 57403 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 29.32 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.1 / Num. measured all: 38681 / Num. unique all: 8387 / Rsym value: 0.554 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementStarting model: PDB entry 3GPG

3gpg


Resolution: 1.9→30.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.879 / SU B: 6.259 / SU ML: 0.087 / SU R Cruickshank DPI: 0.136 / SU Rfree: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2904 5.1 %RANDOM
Rwork0.17 ---
obs0.171 57371 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 111.6 Å2 / Biso mean: 20.065 Å2 / Biso min: 6.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å2-0 Å2
2---0.49 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 144 487 5547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225162
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9917042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21424.104212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04715835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3231534
X-RAY DIFFRACTIONr_chiral_restr0.0910.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213842
X-RAY DIFFRACTIONr_mcbond_it0.6181.53210
X-RAY DIFFRACTIONr_mcangle_it1.14325185
X-RAY DIFFRACTIONr_scbond_it2.29631952
X-RAY DIFFRACTIONr_scangle_it3.6244.51850
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 176 -
Rwork0.308 4067 -
all-4243 -
obs--99.88 %
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)
11.87680.3694-0.07762.10960.95960.71940.1943-0.075-0.28140.2464-0.0394-0.3230.30370.0755-0.1550.26870.0573-0.05440.03550.00250.10788.680737.8674-5.878
21.6090.52930.57272.19460.43982.05360.2241-0.03820.00520.0987-0.2123-0.03710.1679-0.0807-0.01170.19330.00560.03640.02560.0010.02642.376446.8785-7.2061
33.20760.65330.50581.4393-0.37392.88430.26280.05270.00080.0011-0.1049-0.25120.20130.3547-0.15780.15580.01330.00320.0474-0.00720.072414.008850.8369-2.255
418.94651.17082.288811.107211.909912.86230.4924-0.20680.7312-0.27370.1782-0.7128-0.35150.271-0.67060.3126-0.1548-0.10490.29430.07520.249518.821156.28055.0371
51.60080.8837-1.87554.5963-2.99224.31450.0985-0.12110.11830.3213-0.0530.256-0.520.0564-0.04550.11730.0224-0.00560.0573-0.02530.1668-1.949619.1823-5.1052
61.6564-0.21710.01351.53720.70071.36920.01020.1046-0.10480.0319-0.04250.07620.0290.01920.03230.04690.01050.00490.0581-0.00460.08233.80327.4053-11.794
74.3148-0.0497-0.54046.1268-2.395610.44830.09270.04850.1530.05060.09860.4819-0.2098-0.5981-0.19120.06140.0308-0.02610.0966-0.02980.1694-10.633718.3504-9.7298
83.356-3.0965-3.72466.61685.40499.9864-0.062-0.63180.02980.50370.3417-0.38320.54020.3844-0.27970.1338-0.0186-0.08330.15950.05190.135937.09414.083211.6368
93.16440.4650.50851.1340.2631.25980.0528-0.13660.23220.0729-0.07010.0376-0.1027-0.02140.01730.0775-0.0342-0.02730.0284-0.00680.074430.860425.2733.2487
108.2856-3.6345-5.3419.75192.86588.9956-0.0476-0.3959-0.53030.21250.01440.29850.4914-0.38550.03320.1347-0.0908-0.07880.14790.12590.135327.858610.885813.5005
112.64220.9819-0.91942.1216-0.37062.0907-0.20190.1727-0.0927-0.19540.0127-0.19220.0370.16740.18920.1328-0.0803-0.00670.1754-0.01850.1374-18.957937.499911.662
122.99831.7691-0.02751.8321-0.30911.3592-0.12720.15170.2052-0.15320.02870.1759-0.0884-0.01110.09850.0702-0.038-0.03780.0873-0.02920.0814-26.802638.125713.7314
135.6488-3.02680.313810.1870.21045.2513-0.28890.769-0.4017-0.56430.0780.04380.095-0.00530.2110.2509-0.1230.00440.2891-0.07870.0656-23.260533.5087-2.5369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 46
2X-RAY DIFFRACTION2A47 - 120
3X-RAY DIFFRACTION3A121 - 155
4X-RAY DIFFRACTION4A156 - 160
5X-RAY DIFFRACTION5B1 - 10
6X-RAY DIFFRACTION6B11 - 143
7X-RAY DIFFRACTION7B144 - 160
8X-RAY DIFFRACTION8C1 - 9
9X-RAY DIFFRACTION9C10 - 143
10X-RAY DIFFRACTION10C144 - 160
11X-RAY DIFFRACTION11D2 - 34
12X-RAY DIFFRACTION12D35 - 143
13X-RAY DIFFRACTION13D144 - 159

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