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

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Basic information

Entry
Database: PDB / ID: 3gpq
TitleCrystal structure of macro domain of Chikungunya virus in complex with RNA
Components
  • Non-structural protein 3
  • RNA (5'-R(*AP*AP*A)-3')
KeywordsVIRAL PROTEIN/RNA / macro domain / X domain / Chikungunya / alphavirus / virus / VIZIER. Viral enzymes involved in replication / RNA / 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 / VIRAL PROTEIN-RNA complex
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 / nucleoside-triphosphate phosphatase / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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
RNA / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
E: RNA (5'-R(*AP*AP*A)-3')
F: RNA (5'-R(*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)76,4266
Polymers76,4266
Non-polymers00
Water4,504250
1
A: Non-structural protein 3
E: RNA (5'-R(*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)19,5782
Polymers19,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area8000 Å2
MethodPISA
2
B: Non-structural protein 3
F: RNA (5'-R(*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)19,5782
Polymers19,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-2 kcal/mol
Surface area8010 Å2
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)86.824, 86.824, 81.316
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: 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: RNA chain RNA (5'-R(*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
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
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 60011
2PEG 60012
3hepes12

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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
ReflectionResolution: 2→28.421 Å / Num. all: 46210 / Num. obs: 46206 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 35.809 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 0.9 / Num. measured all: 30275 / Num. unique all: 6793 / Rsym value: 0.525 / % possible all: 100

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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
Resolution: 2→28.42 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.224 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.787 / SU B: 11.298 / SU ML: 0.143 / SU R Cruickshank DPI: 0.2 / SU Rfree: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2379 5.2 %RANDOM
Rwork0.215 ---
obs0.218 46173 99.64 %-
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: 29.021 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å2-0 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4744 80 0 250 5074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224784
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9766512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38924.462195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51315725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9651528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213622
X-RAY DIFFRACTIONr_mcbond_it0.6751.53080
X-RAY DIFFRACTIONr_mcangle_it1.18824926
X-RAY DIFFRACTIONr_scbond_it2.15531704
X-RAY DIFFRACTIONr_scangle_it3.5014.51582
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 191 -
Rwork0.297 3267 -
all-3458 -
obs--99.91 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.08380.30840.46061.75420.17062.0001-0.06440.1011-0.01960.01310.1265-0.15470.0710.0975-0.06220.06190.0075-0.0080.081-0.01910.01586.352643.881-5.1527
24.64560.7227-1.63056.1642-0.41056.9092-0.28530.5825-0.0455-0.22540.3412-0.9024-0.0970.631-0.05580.0634-0.07970.01890.3702-0.12880.220920.983549.7085-6.7769
36.79031.0009-0.26284.3258-1.21324.9326-0.1520.3810.4584-0.36720.2189-0.3667-0.68910.5351-0.06690.2955-0.00580.10460.31640.0660.328119.156356.6484.3065
42.1142-1.0087-0.14192.46810.66030.83640.08090.15050.2718-0.2575-0.0507-0.1656-0.2266-0.0585-0.03030.1358-0.0215-0.0010.12470.0120.04175.891714.4115-12.6195
52.1525-0.43690.25431.95570.72281.29030.0010.0529-0.0596-0.0395-0.03330.03060.0591-0.0360.03230.0921-0.01490.00520.0853-0.00210.0032.36085.3234-11.5022
63.8416-1.03640.3493.0033-0.03333.86440.028-0.02570.3642-0.1101-0.05530.3495-0.316-0.35480.02720.10540.0542-0.02640.1154-0.03080.1138-7.808118.0115-9.2813
73.8103-1.41920.87064.8495-1.88762.0524-0.1401-0.27750.38870.1603-0.0189-0.1994-0.13590.1820.15910.1486-0.0402-0.12570.2242-0.12510.522335.777221.30899.9709
82.73110.70992.07970.24280.17286.6332-0.2477-0.2580.31610.0698-0.0560.0527-0.4786-0.06160.30370.46270.0389-0.09390.2103-0.02380.644532.77234.22714.6395
95.60460.6602-0.1780.3221-0.32862.4306-0.1098-0.26020.30540.0236-0.0062-0.3385-0.0996-0.03340.11610.12040.0159-0.08190.0284-0.06420.658928.348522.00131.0397
106.95860.26860.55583.2044-0.67594.5129-0.2322-1.01830.05510.52890.2058-0.46680.5011-0.50890.02640.20370.0303-0.14550.2094-0.08430.315230.35612.625611.4046
114.88330.4265-2.33153.2167-0.98634.7894-0.24730.4311-0.3417-0.54810.09830.53420.4411-0.17940.14910.2011-0.071-0.14760.1953-0.11790.3311-17.918636.036312.0362
123.69692.07540.70721.5627-0.18531.64930.352-0.1694-0.00540.1178-0.10520.39680.1631-0.0882-0.24680.0741-0.049-0.05860.0724-0.09420.5989-22.057636.456920.3582
134.10142.0259-0.22083.2132-0.46691.1974-0.14870.32130.1158-0.18540.07760.52140.0565-0.09820.07110.1219-0.0674-0.1660.2184-0.10550.4711-29.081436.203410.7917
141.05270.4182-1.25854.5675-0.9463.9387-0.2090.4434-0.1218-0.39090.24290.34850.2297-0.2248-0.03390.3511-0.1105-0.19060.2864-0.1320.2837-23.142235.84993.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 139
2X-RAY DIFFRACTION2A140 - 155
3X-RAY DIFFRACTION3A156 - 160
4X-RAY DIFFRACTION4B1 - 39
5X-RAY DIFFRACTION5B40 - 136
6X-RAY DIFFRACTION6B137 - 160
7X-RAY DIFFRACTION7C1 - 25
8X-RAY DIFFRACTION8C27 - 55
9X-RAY DIFFRACTION9C58 - 135
10X-RAY DIFFRACTION10C136 - 159
11X-RAY DIFFRACTION11D2 - 34
12X-RAY DIFFRACTION12D35 - 78
13X-RAY DIFFRACTION13D80 - 126
14X-RAY DIFFRACTION14D127 - 153

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