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- PDB-6vla: Hs05 - Intragenic antimicrobial peptide -

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Basic information

Entry
Database: PDB / ID: 6vla
TitleHs05 - Intragenic antimicrobial peptide
ComponentsIntragenic antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


mRNA N-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / rRNA modification / regulation of centrosome duplication / telomerase holoenzyme complex / N-acetyltransferase activity / rRNA modification in the nucleus and cytosol / protein acetylation ...mRNA N-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / rRNA modification / regulation of centrosome duplication / telomerase holoenzyme complex / N-acetyltransferase activity / rRNA modification in the nucleus and cytosol / protein acetylation / negative regulation of telomere maintenance via telomerase / DNA polymerase binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / small-subunit processome / positive regulation of translation / ribosomal small subunit biogenesis / midbody / tRNA binding / chromosome, telomeric region / nucleolus / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA cytidine acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsSantos, M.A. / Silva, E.M.C. / Brand, G.D. / Oliveira, A.L.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Other governmentFAP-DF: 0193.001566/2017 Brazil
Other governmentFAP-DF: 0193.000866/2015 Brazil
CitationJournal: Materials Science and Engineering C, Materials for Biological Applications
Year: 2020
Title: Characterization of novel human Intragenic Antimicrobial Peptides, incorporation and release studies from ureasil-polyether hybrid matrix
Authors: Mariano, G.H. / Gomes de Sa, L.G. / Carmo da Silva, E.M. / Santos, M.A. / Cardozo Fh, J. / Lira, B.O.V. / Barbosa, E.A. / Araujo, A.R. / Leite, J.R.S.A. / Ramada, M.H.S. / Bloch Jr., C. / ...Authors: Mariano, G.H. / Gomes de Sa, L.G. / Carmo da Silva, E.M. / Santos, M.A. / Cardozo Fh, J. / Lira, B.O.V. / Barbosa, E.A. / Araujo, A.R. / Leite, J.R.S.A. / Ramada, M.H.S. / Bloch Jr., C. / Oliveira, A.L. / Chaker, J.A. / Brand, G.D.
History
DepositionJan 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intragenic antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)2,0661
Polymers2,0661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Intragenic antimicrobial peptide / RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase / N-acetyltransferase 10 / N- ...RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase / N-acetyltransferase 10 / N-acetyltransferase-like protein / hALP


Mass: 2065.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9H0A0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.28 mM peptide, 32 mM D-98% Dodecylphosphorylcholine-d38, 10 mM PBS, 90% H2O/10% D2O
Label: Hs05 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.28 mMpeptidenatural abundance1
32 mMDodecylphosphorylcholine-d38D-98%1
10 mMPBSnatural abundance1
Sample conditionsIonic strength: PBS 10mM Not defined / Label: condition_1 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: distance geometry / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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