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- PDB-6cws: The NMR solution structure of CCL28 -

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Basic information

Entry
Database: PDB / ID: 6cws
TitleThe NMR solution structure of CCL28
ComponentsC-C motif chemokine 28Chemokine
KeywordsCYTOKINE / CCL28 / Chemokine / Antifungal activity
Function / homology
Function and homology information


negative regulation of leukocyte tethering or rolling / cytolysis in another organism / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell-matrix adhesion / response to nutrient / cell chemotaxis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / G alpha (i) signalling events ...negative regulation of leukocyte tethering or rolling / cytolysis in another organism / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell-matrix adhesion / response to nutrient / cell chemotaxis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / killing of cells of another organism / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like
Similarity search - Domain/homology
C-C motif chemokine 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsThomas, M.A. / Peterson, F.C. / Volkman, B.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI120655 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F30 HL134253 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM080202 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: The Solution Structure of CCL28 Reveals Structural Lability that Does Not Constrain Antifungal Activity.
Authors: Thomas, M.A. / He, J. / Peterson, F.C. / Huppler, A.R. / Volkman, B.F.
History
DepositionMar 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.4Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 28


Theoretical massNumber of molelcules
Total (without water)12,3941
Polymers12,3941
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein C-C motif chemokine 28 / Chemokine / Mucosae-associated epithelial chemokine / MEC / Protein CCK1 / Small-inducible cytokine A28


Mass: 12394.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL28, SCYA28 / Plasmid: pET28a
Production host: Aphyosemion etsamense (Escherich's killifish)
Strain (production host): BL21(DE3) / References: UniProt: Q9NRJ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.7 mM [U-99% 13C; U-99% 15N] CCL28, 25 mM [U-99% 2H] MES, 0.02 % sodium azide, 95% H2O/5% D2O
Label: Sample_1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMCCL28[U-99% 13C; U-99% 15N]1
25 mMMES[U-99% 2H]1
0.02 %sodium azidenatural abundance1
Sample conditionsIonic strength: 15 mM / Label: conditions_1 / pH: 6.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600.13 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.6Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures are based on a total of 1487 restraints, 1382 NOE-derived distance constraints and 105 dihedral angle constraints
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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