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- PDB-2kum: Solution structure of the human chemokine CCL27 -

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Basic information

Entry
Database: PDB / ID: 2kum
TitleSolution structure of the human chemokine CCL27
ComponentsC-C motif chemokine 27
KeywordsSIGNALING PROTEIN / CCL27 / CTACK / Chemokine / Cytokine / Disulfide bond / Polymorphism
Function / homology
Function and homology information


: / CCR3 chemokine receptor binding / positive regulation of T cell chemotaxis / Chemokine receptors bind chemokines / chemokine activity / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / cell-cell signaling / G alpha (i) signalling events / killing of cells of another organism ...: / CCR3 chemokine receptor binding / positive regulation of T cell chemotaxis / Chemokine receptors bind chemokines / chemokine activity / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / cell-cell signaling / G alpha (i) signalling events / killing of cells of another organism / immune response / extracellular space / extracellular region
Similarity search - Function
Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics
AuthorsKirkpatrick, J.P. / Jansma, A. / Hsu, A. / Handel, T.M. / Nietlispach, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: NMR analysis of the structure, dynamics, and unique oligomerization properties of the chemokine CCL27.
Authors: Jansma, A.L. / Kirkpatrick, J.P. / Hsu, A.R. / Handel, T.M. / Nietlispach, D.
History
DepositionFeb 22, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 27


Theoretical massNumber of molelcules
Total (without water)10,1661
Polymers10,1661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein C-C motif chemokine 27 / Small-inducible cytokine A27 / CC chemokine ILC / IL-11 R-alpha-locus chemokine / Skinkine / ESkine ...Small-inducible cytokine A27 / CC chemokine ILC / IL-11 R-alpha-locus chemokine / Skinkine / ESkine / Cutaneous T-cell-attracting chemokine / CTACK


Mass: 10165.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALP, CCL27, CTACK, CTAK, ESKINE, ILC, PESKY, SCYA27 / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q9Y4X3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CO)CA
1623D HN(CA)CB
1723D HN(COCA)CB
1823D HN(CA)CO
1923D intra-HNCA
11013D (H)NNH-NOESY
11123D H(CCO)NH
11223D C(CO)NH
11323D (H)CCH-TOCSY
11413D 1H-15N TOCSY
11523D 1H-13C NOESY
11612D 1H-1H NOESY
11723D Me-H(C)CH-TOCSY
11823D Me-(H)CCH-TOCSY
11922D 1H-13C CT-HSQC
12013D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.05 mM [U-15N] CCL27, 0.1 mM [U-2H] EDTA, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-13C; U-15N] CCL27, 0.1 mM [U-2H] EDTA, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.05 mMCCL27[U-15N]1
0.1 mMEDTA[U-2H]1
0.5 mMCCL27[U-13C; U-15N]2
0.1 mMEDTA[U-2H]2
Sample conditionsIonic strength: 0.4 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Biospincollection
Azara2.7Boucher, W. et al.processing
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
ARIA1.2Linge, J.P. et al.structure solution
CNS1.1Brunger, A. et al.structure solution
CNS1.1Brunger, A. et al.refinement
TALOSCornilescu, G. et al.data analysis
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 2568 / NOE intraresidue total count: 814 / NOE long range total count: 108 / NOE medium range total count: 103 / NOE sequential total count: 339 / Hydrogen bond constraints total count: 22 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 44 / Protein psi angle constraints total count: 44
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30
NMR ensemble rmsDistance rms dev: 0.0207 Å / Distance rms dev error: 0.0025 Å

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