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- PDB-2mp1: Solution structure of the human chemokine CCL19 -

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Basic information

Entry
Database: PDB / ID: 2mp1
TitleSolution structure of the human chemokine CCL19
ComponentsC-C motif chemokine 19Chemokine
KeywordsSIGNALING PROTEIN / chemokines / chemokine receptors / CCL19 / CCL21 / CCR7
Function / homology
Function and homology information


positive regulation of dendritic cell dendrite assembly / myeloid dendritic cell chemotaxis / CCR7 chemokine receptor binding / mature conventional dendritic cell differentiation / CCR10 chemokine receptor binding / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / positive regulation of T-helper 1 cell differentiation / establishment of T cell polarity / positive regulation of glycoprotein biosynthetic process ...positive regulation of dendritic cell dendrite assembly / myeloid dendritic cell chemotaxis / CCR7 chemokine receptor binding / mature conventional dendritic cell differentiation / CCR10 chemokine receptor binding / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / positive regulation of T-helper 1 cell differentiation / establishment of T cell polarity / positive regulation of glycoprotein biosynthetic process / chemokine receptor binding / regulation of cell projection assembly / immunological synapse formation / CCR chemokine receptor binding / cell communication / lymphocyte chemotaxis / positive regulation of chemotaxis / negative regulation of dendritic cell apoptotic process / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of cell motility / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / response to nitric oxide / positive regulation of endocytosis / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of protein kinase activity / cellular response to interleukin-1 / positive regulation of T cell proliferation / release of sequestered calcium ion into cytosol / cell maturation / positive regulation of JUN kinase activity / T cell costimulation / positive regulation of interleukin-12 production / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / response to virus / cellular response to virus / positive regulation of GTPase activity / cellular response to type II interferon / positive regulation of receptor-mediated endocytosis / intracellular calcium ion homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Chemokine CC, DCCL motif-cointaining domain / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / 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) ...Chemokine CC, DCCL motif-cointaining domain / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / 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 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Model detailslowest energy, model1
AuthorsVeldkamp, C.T. / Peterson, F.C. / Gabel-Eissens, S.J. / Gillitzer, M.L.
CitationJournal: Biochemistry / Year: 2015
Title: Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.
Authors: Veldkamp, C.T. / Kiermaier, E. / Gabel-Eissens, S.J. / Gillitzer, M.L. / Lippner, D.R. / DiSilvio, F.A. / Mueller, C.J. / Wantuch, P.L. / Chaffee, G.R. / Famiglietti, M.W. / Zgoba, D.M. / ...Authors: Veldkamp, C.T. / Kiermaier, E. / Gabel-Eissens, S.J. / Gillitzer, M.L. / Lippner, D.R. / DiSilvio, F.A. / Mueller, C.J. / Wantuch, P.L. / Chaffee, G.R. / Famiglietti, M.W. / Zgoba, D.M. / Bailey, A.A. / Bah, Y. / Engebretson, S.J. / Graupner, D.R. / Lackner, E.R. / LaRosa, V.D. / Medeiros, T. / Olson, M.L. / Phillips, A.J. / Pyles, H. / Richard, A.M. / Schoeller, S.J. / Touzeau, B. / Williams, L.G. / Sixt, M. / Peterson, F.C.
History
DepositionMay 9, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 19


Theoretical massNumber of molelcules
Total (without water)8,8141
Polymers8,8141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein C-C motif chemokine 19 / Chemokine / Beta-chemokine exodus-3 / CK beta-11 / Epstein-Barr virus-induced molecule 1 ligand chemokine / ...Beta-chemokine exodus-3 / CK beta-11 / Epstein-Barr virus-induced molecule 1 ligand chemokine / EBI1 ligand chemokine / ELC / Macrophage inflammatory protein 3 beta / MIP-3-beta / Small-inducible cytokine A19


Mass: 8814.282 Da / Num. of mol.: 1 / Fragment: CCL19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL19, ELC, MIP3B, SCYA19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99731

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: .515 mM [U-100% 13C; U-100% 15N] Human Chemokine CCL19, 10 % [U-99% 2H] D2O, 25 mM [U-100% 2H] dueterated MES, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
.515 mMHuman Chemokine CCL19-1[U-100% 13C; U-100% 15N]1
10 %D2O-2[U-99% 2H]1
25 mMdueterated MES-3[U-100% 2H]1
Sample conditionsIonic strength: 6 mM / pH: 5.6 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin3.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CARA1.8.4Keller, R.data analysis
CYANA3.1Guntert, P.refinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE ...Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: CCL19 STRUCTURES ARE BASED ON A TOTAL OF 2481 NOE CONSTRAINTS ( 1559 INTRA, 398 SEQUENTIAL, 171 MEDIUM, 353 LONG RANGE) AND 85 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS., CCL19 STRUCTURES ARE ...Details: CCL19 STRUCTURES ARE BASED ON A TOTAL OF 2481 NOE CONSTRAINTS ( 1559 INTRA, 398 SEQUENTIAL, 171 MEDIUM, 353 LONG RANGE) AND 85 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS., CCL19 STRUCTURES ARE BASED ON A TOTAL OF 2481 NOE CONSTRAINTS ( 1559 INTRA, 398 SEQUENTIAL, 171 MEDIUM, 353 LONG RANGE) AND 85 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 2481 / NOE intraresidue total count: 1559 / NOE long range total count: 353 / NOE medium range total count: 171 / NOE sequential total count: 398
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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