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- PDB-4tu0: CRYSTAL STRUCTURE OF CHIKUNGUNYA VIRUS NSP3 MACRO DOMAIN IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 4tu0
TitleCRYSTAL STRUCTURE OF CHIKUNGUNYA VIRUS NSP3 MACRO DOMAIN IN COMPLEX WITH A 2'-5' OLIGOADENYLATE TRIMER
Components
  • 2'-5' OLIGOADENYLATE TRIMER
  • Non-structural polyprotein 3
KeywordsVIRAL PROTEIN / STRUCTURAL GENOMICS / MARSEILLES STRUCTURAL GENOMICS PROGRAM AT AFMB / MSGP / ATP-BINDING / CYTOPLASM / HELICASE / HYDROLASE / MEMBRANE / NUCLEOTIDE-BINDING / NUCLEOTIDYLTRANSFERASE / RNA REPLICATION / RNA-BINDING / RNA-DIRECTED RNA POLYMERASE
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
DI(HYDROXYETHYL)ETHER / RNA / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMorin, B. / Ferron, f.p. / Malet, h. / Coutard, b. / Canard, b.
CitationJournal: TO BE PUBLISHED
Title: CRYSTAL STRUCTURE OF CHIKUNGUNYA VIRUS NSP3 MACRO DOMAIN IN COMPLEX WITH A 2'-5' OLIGOADENYLATE TRIMER
Authors: Morin, B. / Ferron, F.P. / Malet, H. / Coutard, B. / Canard, B.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Advisory / Data collection / Database references
Category: citation_author / pdbx_seq_map_depositor_info / pdbx_validate_polymer_linkage
Item: _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn
Revision 1.3Dec 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural polyprotein 3
B: Non-structural polyprotein 3
C: Non-structural polyprotein 3
D: Non-structural polyprotein 3
F: 2'-5' OLIGOADENYLATE TRIMER
G: 2'-5' OLIGOADENYLATE TRIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9588
Polymers76,7466
Non-polymers2122
Water3,927218
1
A: Non-structural polyprotein 3
G: 2'-5' OLIGOADENYLATE TRIMER


Theoretical massNumber of molelcules
Total (without water)19,7382
Polymers19,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area8510 Å2
MethodPISA
2
B: Non-structural polyprotein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7412
Polymers18,6351
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint2 kcal/mol
Surface area8280 Å2
MethodPISA
3
C: Non-structural polyprotein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7412
Polymers18,6351
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint3 kcal/mol
Surface area8040 Å2
MethodPISA
4
D: Non-structural polyprotein 3
F: 2'-5' OLIGOADENYLATE TRIMER


Theoretical massNumber of molelcules
Total (without water)19,7382
Polymers19,7382
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-6 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.371, 87.371, 84.662
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 polyprotein 3 / nsP3


Mass: 18635.123 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1334-1493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: S27-African prototype / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7 EXPRESS IQ (BIOLABS-C3016)
References: UniProt: Q8JUX6, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'- ...References: UniProt: Q8JUX6, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'-phosphatase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase
#2: RNA chain 2'-5' OLIGOADENYLATE TRIMER / RNA (2'-R(*AP*AP*ATP)-5'')


Mass: 1102.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 46% PEG 600, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 7.4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.86 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 2.3→75.67 Å / Num. obs: 32115 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Net I/σ(I): 0
Reflection shellResolution: 2.3→2.42 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0044refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GPG

3gpg


Resolution: 2.3→75.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.272 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1594 5.1 %RANDOM
Rwork0.174 ---
obs0.177 29865 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→75.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 149 14 218 5322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225334
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9997261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34623.75224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46515890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4881540
X-RAY DIFFRACTIONr_chiral_restr0.1120.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213997
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9291.53268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74325281
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.74232066
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4684.51979
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 120 -
Rwork0.212 2139 -
obs--96.75 %

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