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- PDB-7p27: NMR solution structure of Chikungunya virus macro domain -

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Basic information

Entry
Database: PDB / ID: 7p27
TitleNMR solution structure of Chikungunya virus macro domain
ComponentsPolyprotein P1234
KeywordsVIRAL PROTEIN / CHIKV / macro domain / viral replication / ADP-ribose
Function / homology
Function and homology information


ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / regulation of cytoskeleton organization ...ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide adenylyltransferase / polynucleotide 5'-phosphatase activity / 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 / 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 / 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 / (+) 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
Similarity search - Domain/homology
Biological speciesChikungunya virus
MethodSOLUTION NMR / molecular dynamics
AuthorsLykouras, M.V. / Tsika, A.C. / Papageorgiou, N. / Canard, B. / Coutard, B. / Bentrop, D. / Spyroulias, G.A.
Funding support Greece, France, 3items
OrganizationGrant numberCountry
European Research Council (ERC)EU FP7 REGPOT CT-2011-285950 SEE-DRUG Greece
European Commission653316 France
European Regional Development FundMIS 5002550 Greece
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity.
Authors: Tsika, A.C. / Gallo, A. / Fourkiotis, N.K. / Argyriou, A.I. / Sreeramulu, S. / Lohr, F. / Rogov, V.V. / Richter, C. / Linhard, V. / Gande, S.L. / Altincekic, N. / Krishnathas, R. / Elamri, I. ...Authors: Tsika, A.C. / Gallo, A. / Fourkiotis, N.K. / Argyriou, A.I. / Sreeramulu, S. / Lohr, F. / Rogov, V.V. / Richter, C. / Linhard, V. / Gande, S.L. / Altincekic, N. / Krishnathas, R. / Elamri, I. / Schwalbe, H. / Wollenhaupt, J. / Weiss, M.S. / Spyroulias, G.A.
History
DepositionJul 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: pdbx_database_status / struct_ref
Item: _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyprotein P1234


Theoretical massNumber of molelcules
Total (without water)18,6351
Polymers18,6351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9080 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 21all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein Polyprotein P1234 / P1234 / Non-structural polyprotein


Mass: 18635.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 8 residues are not shown and correspond to sequence MKHHHHHH
Source: (gene. exp.) Chikungunya virus (strain S27-African prototype)
Strain: S27-African prototype / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q8JUX6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic13D HBHA(CO)NH
141isotropic13D HNHA
152isotropic13D CBCA(CO)NH
192isotropic13D HN(CA)CB
182isotropic13D HNCA
172isotropic13D HN(CO)CA
162isotropic13D HNCO
1112isotropic13D HN(CA)CO
1102isotropic13D (H)CCH-TOCSY
1122isotropic13D 1H-13C NOESY aliphatic
1132isotropic13D 1H-13C NOESY aromatic
1141isotropic13D 1H-15N NOESY
1153isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.6 mM [U-99% 15N] Chikungunya virus macro domain, 20 mM no sodium chloride, 10 mM no HEPES, 2 mM no DTT, 2 mM no EDTA, 0.25 mM no DSS, 10 % no D2O, 90% H2O/10% D2OCHIKV macro domain, [U-99% 15N], 0.6 mM; soduim chloride 20 mM; Hepes 10 mM15N90% H2O/10% D2O
solution20.6 mM [U-99% 13C; U-99% 15N] Chikungunya virus macro domain, 20 mM no sodium chloride, 10 mM no HEPES, 2 mM no DTT, 2 mM no EDTA, 0.25 mM no DSS, 10 % no D2O, 90% H2O/10% D2OCHIKV macro domain, [U-99% 13C; U-99% 15N], 0.6 mM; soduim chloride 20 mM; Hepes 10 mM13C-15N90% H2O/10% D2O
solution30.3 mM no Chikungunya virus macro domain, 20 mM no sodium chloride, 2 mM no HEPES, 2 mM no DTT, 2 mM no EDTA, 0.25 mM no DSS, 10 % no D2O, 90% H2O/10% D2Ounlabeled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMChikungunya virus macro domain[U-99% 15N]1
20 mMsodium chlorideno1
10 mMHEPESno1
2 mMDTTno1
2 mMEDTAno1
0.25 mMDSSno1
10 %D2Ono1
0.6 mMChikungunya virus macro domain[U-99% 13C; U-99% 15N]2
20 mMsodium chlorideno2
10 mMHEPESno2
2 mMDTTno2
2 mMEDTAno2
0.25 mMDSSno2
10 %D2Ono2
0.3 mMChikungunya virus macro domainno3
20 mMsodium chlorideno3
2 mMHEPESno3
2 mMDTTno3
2 mMEDTAno3
0.25 mMDSSno3
10 %D2Ono3
Sample conditionsIonic strength: 20 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance HD III H 700 / Manufacturer: Bruker / Model: Avance HD III H 700 / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARAv1.5.5Keller and Wuthrichpeak picking
CARAv1.5.5Keller and Wuthrichchemical shift assignment
DYANAGuntert, Braun and Wuthrichstructure calculation
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 21 / Conformers submitted total number: 21

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