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- PDB-6mbm: HS02 - Intragenic antimicrobial peptides derived from the protein... -

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Basic information

Entry
Database: PDB / ID: 6mbm
TitleHS02 - Intragenic antimicrobial peptides derived from the protein unconventional myosin 1h
ComponentsUnconventional myosin-Ih peptide
KeywordsANTIMICROBIAL PROTEIN / pro-inflammatory mediators / migration of fibroblasts
Function / homology
Function and homology information


microfilament motor activity => GO:0000146 / vesicle transport along actin filament / myosin complex / microfilament motor activity / microvillus / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / ATP binding ...microfilament motor activity => GO:0000146 / vesicle transport along actin filament / myosin complex / microfilament motor activity / microvillus / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site ...Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-Ih
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsSantos, M.A. / Brand, G.D. / Oliveira, A.L.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Foundation for Research Support of the Federal District - Government of BrasiliaFAP-DF: 0193.001566/2017 Brazil
Foundation for Research Support of the Federal District - Government of BrasiliaFAP-DF: 0193.000866/2015 Brazil
CitationJournal: Plos One / Year: 2019
Title: Intragenic antimicrobial peptides (IAPs) from human proteins with potent antimicrobial and anti-inflammatory activity.
Authors: Brand, G.D. / Ramada, M.H.S. / Manickchand, J.R. / Correa, R. / Ribeiro, D.J.S. / Santos, M.A. / Vasconcelos, A.G. / Abrao, F.Y. / Prates, M.V. / Murad, A.M. / Cardozo Fh, J.L. / Leite, J.R. ...Authors: Brand, G.D. / Ramada, M.H.S. / Manickchand, J.R. / Correa, R. / Ribeiro, D.J.S. / Santos, M.A. / Vasconcelos, A.G. / Abrao, F.Y. / Prates, M.V. / Murad, A.M. / Cardozo Fh, J.L. / Leite, J.R.S.A. / Magalhaes, K.G. / Oliveira, A.L. / Bloch Jr., C.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-Ih peptide


Theoretical massNumber of molelcules
Total (without water)1,9671
Polymers1,9671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1890 Å2
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 Unconventional myosin-Ih peptide / Myosin-1H


Mass: 1967.469 Da / Num. of mol.: 1 / Fragment: residues 751-766 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8N1T3

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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
141isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 2 uM peptide, 50 uM D-98% Dodecylphosphorylcholine-d38, 10 mM PBS, 90% H2O/10% D2O
Label: HS02 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 uMpeptidenatural abundance1
50 uMDodecylphosphorylcholine-d38D-98%1
10 mMPBSnatural abundance1
Sample conditionsIonic strength: PBS 10mM Not defined / Label: conditions_1 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / 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
NameVersionDeveloperClassification
ARIA2.3.1Linge, O'Donoghue and Nilgesrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNMR2.4CCPNchemical shift assignment
CcpNMR2.4CCPNpeak picking
ARIA2.3.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: distance geometry / Software ordinal: 1
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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