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- PDB-8yd6: Solution structure of peptide H30 by Nuclear Magnetic Resonance S... -

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Basic information

Entry
Database: PDB / ID: 8yd6
TitleSolution structure of peptide H30 by Nuclear Magnetic Resonance Spectroscopy
ComponentsDefensin beta 4A
KeywordsANTIMICROBIAL PROTEIN / Cationic peptides / antiviral / virus-binding / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis ...CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Beta defensin type / Beta defensin / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsSze, K.H. / Zhao, H.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
Other governmentInnoHK Hong Kong
Other governmentHMRF-2020-CID-HKU1-8 Hong Kong
CitationJournal: To Be Published
Title: Solution structure of H30 peptide by NMR spectroscopy
Authors: Sze, K.H. / Zhao, H.
History
DepositionFeb 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin beta 4A


Theoretical massNumber of molelcules
Total (without water)3,2701
Polymers3,2701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Defensin beta 4A / Beta-defensin 2 / BD-2 / hBD-2 / Defensin / beta 2 / Skin-antimicrobial peptide 1 / SAP1


Mass: 3270.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15263
Has protein modificationY

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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 COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 0.9 mM H30, 13 mM TCEP.HCl, 0.175 mM 98%[U-2H]2,2,3,3-D4 TSP, 90% H2O/10% D2O
Details: 0.9mM H30 in 90%H2O/10%D2O with 13mM TCEP as disulphide bond reducing agent
Label: H30 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMH30natural abundance1
13 mMTCEP.HClnatural abundance1
0.175 mMTSP98%[U-2H]2,2,3,3-D41
Sample conditionsDetails: TCEP was added to reduce intermolecular disulphide bonds
Ionic strength: 0 Not defined / Label: 1 / pH: 2.5 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: PASEI probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
Sparky3.106Goddardpeak picking
Sparky3.106Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Sparky3.106Goddardchemical shift assignment
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics5The structures are based on 311 NOE-derived distance constraints and 195 dihedral angle restraints
simulated annealing6Energy minimization with water solvent refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20

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