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

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Basic information

Entry
Database: PDB / ID: 5mqx
TitleNMR solution structure of macro domain from Venezuelan equine encephalitis virus(VEEV) in complex with ADP-ribose
ComponentsNon-structural protein3
KeywordsVIRAL PROTEIN / macro domain / Venezuelan equine encephalitis virus / Alphavirus / ADP-ribose / non-structural protein 3
Function / homology
Function and homology information


O-acetyl-ADP-ribose deacetylase 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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...O-acetyl-ADP-ribose deacetylase 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 / 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 / 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 / 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. / Leucine Aminopeptidase, subunit E, domain 1 ...: / : / : / 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. / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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 / (+) 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
ADENOSINE-5-DIPHOSPHORIBOSE / Polyprotein P1234
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus
MethodSOLUTION NMR / molecular dynamics
AuthorsMakrynitsa, G.I. / Ntonti, D. / Marousis, K.D. / Matsoukas, M.T. / Papageorgiou, N. / Coutard, B. / Bentrop, D. / Spyroulias, G.A.
Funding support1items
OrganizationGrant numberCountry
285950
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.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: 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 protein3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6642
Polymers18,1041
Non-polymers5591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area900 Å2
ΔGint-8 kcal/mol
Surface area7930 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 112target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Non-structural protein3


Mass: 18104.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain P676)
Gene: NSP3 / Plasmid: pDest14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
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
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2

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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
121isotropic13D 1H-15N NOESY
132isotropic13D CBCA(CO)NH
142isotropic13D HN(CA)CB
152isotropic13D HNCO
162isotropic13D HN(CA)CO
172isotropic13D HNCA
182isotropic13D HN(CO)CA
191isotropic13D HNHA
1102isotropic13D (H)CCH-TOCSY
1112isotropic12D 1H-13C HSQC
1122isotropic13D 1H-13C NOESY aliphatic
1132isotropic13D 1H-13C NOESY aromatic
1142isotropic12D 13C filtered/edited NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.18 mM [U-99% 15N] VEEV macro domain, 0.2 mM ADENOSINE-5-DIPHOSPHORIBOSE, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.21 mM [U-99% 13C; U-99% 15N] VEEV macro domain, 0.26 mM ADENOSINE-5-DIPHOSPHORIBOSE, 90% H2O/10% D2O13C/15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.18 mMVEEV macro domain[U-99% 15N]1
0.2 mMADENOSINE-5-DIPHOSPHORIBOSEnatural abundance1
0.21 mMVEEV macro domain[U-99% 13C; U-99% 15N]2
0.26 mMADENOSINE-5-DIPHOSPHORIBOSEnatural abundance2
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 7.0 / 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
Details: cryogenically cooled 5mm 1H/13C/15N/D Z-gradient probe (TCI)

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
CARA1.5.5Keller and Wuthrichchemical shift assignment
DYANAGuntert, Braun and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 112 / Conformers submitted total number: 21

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