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Yorodumi- PDB-5isn: NMR solution structure of macro domain from Venezuelan equine enc... -
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-Basic information
Entry | Database: PDB / ID: 5isn | |||||||||
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Title | NMR solution structure of macro domain from Venezuelan equine encephalitis virus | |||||||||
Components | Non-structural polyprotein | |||||||||
Keywords | VIRAL PROTEIN / viral macro domain / ADP-ribose-binding module / Alphavirus / NMR spectroscopy / Venezuelan equine encephalitis virus / transferase | |||||||||
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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping ...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 | |||||||||
Biological species | Venezuelan equine encephalitis virus | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Makrynitsa, G.I. / Ntonti, D. / Marousis, K.D. / Tsika, A.C. / Papageorgiou, N. / Coutard, B. / Bentrop, D. / Spyroulias, G.A. | |||||||||
Funding support | 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5isn.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5isn.ent.gz | 942.3 KB | Display | PDB format |
PDBx/mmJSON format | 5isn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/5isn ftp://data.pdbj.org/pub/pdb/validation_reports/is/5isn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 20 mM / Label: conditions_sample1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 6 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 21 / Conformers submitted total number: 21 |