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- PDB-5ki0: NMR structure of human antimicrobial peptide KAMP-19 -

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Basic information

Entry
Database: PDB / ID: 5ki0
TitleNMR structure of human antimicrobial peptide KAMP-19
ComponentsAntimicrobial peptide KAMP-19
KeywordsANTIMICROBIAL PROTEIN / Keratin 6A fragment / non-alpha beta structure
Function / homology
Function and homology information


: / keratin filament / Keratinization / negative regulation of entry of bacterium into host cell / Formation of the cornified envelope / cytolysis by host of symbiont cells / morphogenesis of an epithelium / wound healing / structural constituent of cytoskeleton / antimicrobial humoral immune response mediated by antimicrobial peptide ...: / keratin filament / Keratinization / negative regulation of entry of bacterium into host cell / Formation of the cornified envelope / cytolysis by host of symbiont cells / morphogenesis of an epithelium / wound healing / structural constituent of cytoskeleton / antimicrobial humoral immune response mediated by antimicrobial peptide / cell differentiation / defense response to Gram-positive bacterium / positive regulation of cell population proliferation / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
Keratin, type II / Keratin type II head / Keratin type II head / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein
Similarity search - Domain/homology
Keratin, type II cytoskeletal 6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105147 United States
CitationJournal: Front Microbiol / Year: 2016
Title: Membrane-Active Epithelial Keratin 6A Fragments (KAMPs) Are Unique Human Antimicrobial Peptides with a Non-alpha beta Structure.
Authors: Lee, J.T. / Wang, G. / Tam, Y.T. / Tam, C.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Data collection / Database references
Revision 1.2Aug 9, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_number_of_molecules
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jun 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 1.6May 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

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Assembly

Deposited unit
A: Antimicrobial peptide KAMP-19


Theoretical massNumber of molelcules
Total (without water)1,7691
Polymers1,7691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Antimicrobial peptide KAMP-19


Mass: 1768.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02538*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D DQF-COSY
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: micelle / Contents: 3.4 mM KAMP-19, 90% H2O/10% D2O
Details: The peptide was solubilized with deuterated SDS at a peptide/SDS molar ratio of 1:60, pH 5.4
Label: 1H sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 3.4 mM / Component: KAMP-19 / Isotopic labeling: natural abundance
Sample conditionsDetails: The peptide was solubilized with deuterated SDS at a peptide/SDS molar ratio of 1:60,
Ionic strength: nd Not defined / Ionic strength err: 0.2 / Label: condition_1 / pH: 5.4 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz / Details: cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH1G. Marius Clore (NIH)structure calculation
PIPPGarrettchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
PIPPGarrettrefinement
RefinementMethod: simulated annealing / Software ordinal: 4 / Details: High and low temperature
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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