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- PDB-5iq5: NMR solution structure of Mayaro virus macro domain -

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Basic information

Entry
Database: PDB / ID: 5iq5
TitleNMR solution structure of Mayaro virus macro domain
ComponentsMacro domain
KeywordsVIRAL PROTEIN / viral macro domains / Mayaro virus / Alphavirus / ADP ribose binding module
Function / homology
Function and homology information


chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / ADP-ribose 1''-phosphate phosphatase / host cell filopodium / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase ...chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader 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 speciesMayaro virus
MethodSOLUTION NMR / molecular dynamics
AuthorsMelekis, E. / Tsika, A.C. / Bentrop, D. / Papageorgiou, N. / Coutard, B. / Spyroulias, G.A.
Funding support2items
OrganizationGrant numberCountry
European Union285950
European Union228292
Citation
Journal: J.Mol.Biol. / Year: 2019
Title: Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain.
Authors: Tsika, A.C. / Melekis, E. / Tsatsouli, S.A. / Papageorgiou, N. / Mate, M.J. / Canard, B. / Coutard, B. / Bentrop, D. / Spyroulias, G.A.
#1: 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.
#2: 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.
#3: Journal: Zeitschfrift fur Kristallographie / Year: 2010
Title: Preliminary insights into the non structural protein 3 macro domain of the Mayaro virus by powder diffraction
Authors: Papageorgiou, N. / Watier, Y. / Saunders, L. / Coutard, B. / Lantez, V. / Gould, E.A. / Fitch, A.N. / Wright, J.P. / Canard, B. / Margiolaki, I.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Sep 11, 2019Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.6Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macro domain


Theoretical massNumber of molelcules
Total (without water)18,1471
Polymers18,1471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8800 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 21target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Macro domain / Polyprotein nsP1234 / P1234


Mass: 18147.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mayaro virus (strain Brazil) / Details (production host): Gateway cloning system / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2, pLysS, DL39
References: UniProt: Q8QZ73, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'- ...References: UniProt: Q8QZ73, 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
522isotropic12D 1H-15N HSQC
5172isotropic13D 1H-15N NOESY
5152isotropic13D HNHA
533isotropic13D CBCA(CO)NH
5193isotropic13D 1H-13C NOESY aliphatic
5183isotropic13D 1H-13C NOESY aromatic
5113isotropic13D HNCO
5203isotropic13D HN(CA)CO
5103isotropic13D HNCA
5143isotropic13D (H)CCH-TOCSY
5133isotropic13D HN(CO)CA
5213isotropic12D 1H-13C HSQC
5243isotropic13D 1H-13C NOESY
5223isotropic12D 1H-13C HSQC
5122isotropic12D 1H-15N HSQC TROSY
593isotropic13D HN(CA)CB
583isotropic13D HBHA(CO)NH
544isotropic22D 1H-15N HSQC
555isotropic22D 1H-15N HSQC
567isotropic13D HN(CA)CB
671isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.4 mM Mayaro virus' macro domain, 90% H2O/10% D2O10mM Hepes 20mM NaCl 2mM DTT pH 71H_sample90% H2O/10% D2O
solution20.4 mM [U-99% 15N] Mayaro virus' macro domain, 90% H2O/10% D2O10mM Hepes 20mM NaCl 2mM DTT pH 715N_sample90% H2O/10% D2O
solution30.4 mM [U-99% 13C; U-99% 15N] Mayaro virus' macro domain, 90% H2O/10% D2O10mM Hepes 20mM NaCl 2mM DTT pH 715N_13C_sample90% H2O/10% D2O
solution40.4 mM [U-15N]-Ala-Leu-Val Mayaro virus' macro domain, 90% H2O/10% D2O10mM Hepes 20mM NaCl 2mM DTT pH 7Specific Labeling 15N Ala-Leu-Val90% H2O/10% D2O
solution50.4 mM [U-14N]-Arg Mayaro virus' macro domain, 90% H2O/10% D2O10mM Hepes 20mM NaCl 2mM DTT pH 7Reverse Labelong 14N Arg90% H2O/10% D2O
solution60.4 mM [U-14N]-Asn-Cys Mayaro virus' macro domain, 90% H2O/10% D2O10mM Hepes 20mM NaCl 2mM DTT pH 7Reverse Labelong 14N Asn-Cys90% H2O/10% D2O
solution70.4 mM [U-100% 13C; U-100% 15N; U-80% 2H] Mayaro virus' macro domain, 90% H2O/10% D2O10mM Hepes 20mM NaCl 2mM DTT pH 7Deuterated90% H2O/10% D2O
solution80.5 mM Mayaro virus' macro domain, 90% H2O/10% D2O2mM Hepes 20mM NaCl 2mM DTT pH 71H_2sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMMayaro virus' macro domainnatural abundance1
0.4 mMMayaro virus' macro domain[U-99% 15N]2
0.4 mMMayaro virus' macro domain[U-99% 13C; U-99% 15N]3
0.4 mMMayaro virus' macro domain[U-15N]-Ala-Leu-Val4
0.4 mMMayaro virus' macro domain[U-14N]-Arg5
0.4 mMMayaro virus' macro domain[U-14N]-Asn-Cys6
0.4 mMMayaro virus' macro domain[U-100% 13C; U-100% 15N; U-80% 2H]7
0.5 mMMayaro virus' macro domainnatural abundance8
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
510mM Hepes 20mM NaCl 2mM DTT20 mMconditions71 atm298 K
62mM Hepes 20mM NaCl 2mM DTT20 mMcondition_871 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001equipped with a cryogenically cooled pulsed-field gradient triple-resonance probe (TXI)
Bruker AVANCEBrukerAVANCE7002equipped with a cryogenically cooled 5 mm 1H/13C/15N/D Z-gradient probe (TCI). Avance III High-Definition four-channel

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.3Bruker Biospincollection
TopSpin3.2Bruker Biospincollection
TopSpin3.3Bruker Biospinprocessing
TopSpin3.2Bruker Biospinprocessing
CARA1.5.5Keller and Wuthrichchemical shift assignment
XEASYBartels et al.peak picking
DYANAGuntert, Braun and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 9
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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