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- PDB-5isn: NMR solution structure of macro domain from Venezuelan equine enc... -

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Basic information

Entry
Database: PDB / ID: 5isn
TitleNMR solution structure of macro domain from Venezuelan equine encephalitis virus
ComponentsNon-structural polyprotein
KeywordsVIRAL PROTEIN / viral macro domain / ADP-ribose-binding module / Alphavirus / NMR spectroscopy / Venezuelan equine encephalitis virus / transferase
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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / 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 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
Biological speciesVenezuelan equine encephalitis virus
MethodSOLUTION NMR / molecular dynamics
AuthorsMakrynitsa, G.I. / Ntonti, D. / Marousis, K.D. / Tsika, A.C. / Papageorgiou, N. / Coutard, B. / Bentrop, D. / Spyroulias, G.A.
Funding support2items
OrganizationGrant numberCountry
European Union285950
European Union228292
Citation
Journal: J.Struct.Biol. / Year: 2019
Title: Conformational plasticity of the VEEV macro domain is important for binding of ADP-ribose.
Authors: Makrynitsa, G.I. / Ntonti, D. / Marousis, K.D. / Birkou, M. / Matsoukas, M.T. / Asami, S. / Bentrop, D. / Papageorgiou, N. / Canard, B. / Coutard, B. / Spyroulias, G.A.
#1: Journal: Biomol NMR Assign / Year: 2015
Title: NMR study of non-structural proteins--part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).
Authors: Makrynitsa, G.I. / Ntonti, D. / Marousis, K.D. / Tsika, A.C. / Lichiere, J. / Papageorgiou, N. / Coutard, B. / Bentrop, D. / Spyroulias, G.A.
#2: Journal: Biomol NMR Assign / Year: 2015
Title: NMR study of non-structural proteins--part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV).
Authors: Melekis, E. / Tsika, A.C. / Lichiere, J. / Chasapis, C.T. / Margiolaki, I. / Papageorgiou, N. / Coutard, B. / Bentrop, D. / Spyroulias, G.A.
#3: Journal: 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 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural polyprotein


Theoretical massNumber of molelcules
Total (without water)18,3651
Polymers18,3651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9250 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 21target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Non-structural polyprotein / Polyprotein nsP1234 / P1234


Mass: 18364.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain P676)
Strain: P676 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 (pLysS) DL39
References: UniProt: P36328, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'- ...References: UniProt: P36328, 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

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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
121isotropic12D 1H-15N HSQC TROSY
132isotropic13D HN(CA)CB
142isotropic13D HN(CA)CB TROSY
152isotropic13D HN(CA)CO
162isotropic13D HN(CA)CO TROSY
171isotropic13D HNHA
182isotropic13D HNCO
192isotropic13D HN(CO)CA
1102isotropic13D HNCA
1112isotropic13D CBCA(CO)NH
1121isotropic13D HBHA(CO)NH
1132isotropic13D (H)CCH-TOCSY
1142isotropic12D 1H-13C HSQC
1151isotropic13D 1H-15N NOESY
1162isotropic13D 1H-13C NOESY aliphatic
1172isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.4 mM [U-99% 15N] Veev macro domain, 90% H2O/10% D2O10mM HEPES, 20mM NaCl, 2mM DTT15N_sample90% H2O/10% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] Veev macro domain, 90% H2O/10% D2O10mM HEPES, 20mM NaCl, 2mM DTT13C_15N_sample90% H2O/10% D2O
solution30.01 mM [U-15N]-Leu-Ala-Val Veev macro domain, 90% H2O/10% D2O10mM HEPES, 20mM NaCl, 2mM DTT15N_sample_LAV90% H2O/10% D2O
solution40.02 mM [U-14N]-Lys Veev macro domain, 90% H2O/10% D2O10mM HEPES, 20mM NaCl, 2mM DTT15N_sample-K90% H2O/10% D2O
solution50.3 mM Veev macro domain, 90% H2O/10% D2O10mM HEPES, 20mM NaCl, 2mM DTT1H_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMVeev macro domain[U-99% 15N]1
0.8 mMVeev macro domain[U-99% 13C; U-99% 15N]2
0.01 mMVeev macro domain[U-15N]-Leu-Ala-Val3
0.02 mMVeev macro domain[U-14N]-Lys4
0.3 mMVeev macro domainnatural abundance5
Sample conditionsIonic strength: 20 mM / Label: conditions_sample1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
CARA1.5.5Keller and Wuthrichchemical shift assignment
XEASYBartels et al.peak picking
DYANAGuntert, Braun and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 21 / Conformers submitted total number: 21

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