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- PDB-2l4n: Solution Structure of the Chemokine CCL21 -

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Basic information

Entry
Database: PDB / ID: 2l4n
TitleSolution Structure of the Chemokine CCL21
ComponentsC-C motif chemokine 21
KeywordsCYTOKINE / SLC / 6Ckine / Exodus-2 / CCR7 / Chemokine
Function / homology
Function and homology information


mesangial cell-matrix adhesion / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / CCR7 chemokine receptor binding / positive regulation of myeloid dendritic cell chemotaxis / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / negative regulation of leukocyte tethering or rolling / establishment of T cell polarity ...mesangial cell-matrix adhesion / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / CCR7 chemokine receptor binding / positive regulation of myeloid dendritic cell chemotaxis / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / negative regulation of leukocyte tethering or rolling / establishment of T cell polarity / positive regulation of glycoprotein biosynthetic process / chemokine receptor binding / immunological synapse formation / positive regulation of T cell chemotaxis / positive regulation of pseudopodium assembly / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of chemotaxis / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / ruffle organization / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / positive regulation of cell motility / chemokine activity / positive regulation of cell adhesion mediated by integrin / dendritic cell chemotaxis / positive regulation of filopodium assembly / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / monocyte chemotaxis / positive regulation of T cell migration / cellular response to interleukin-1 / release of sequestered calcium ion into cytosol / cell maturation / T cell costimulation / neutrophil chemotaxis / cell chemotaxis / positive regulation of JNK cascade / cellular response to type II interferon / positive regulation of receptor-mediated endocytosis / cell-cell signaling / 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 / 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 21
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
Model detailslowest energy, model 1
AuthorsVeldkamp, C.T. / Peterson, F.C. / Love, M. / Sandberg, J.L.
CitationJournal: Biochemistry / Year: 2012
Title: Solution structure of CCL21 and identification of a putative CCR7 binding site.
Authors: Love, M. / Sandberg, J.L. / Ziarek, J.J. / Gerarden, K.P. / Rode, R.R. / Jensen, D.R. / McCaslin, D.R. / Peterson, F.C. / Veldkamp, C.T.
History
DepositionOct 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 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 21


Theoretical massNumber of molelcules
Total (without water)12,5201
Polymers12,5201
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein C-C motif chemokine 21 / 6Ckine / Beta-chemokine exodus-2 / Secondary lymphoid-tissue chemokine / SLC / Small-inducible cytokine A21


Mass: 12519.618 Da / Num. of mol.: 1 / Fragment: CCL21 (UNP RESIDUES 24-134)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL21, RP11-195F19.22-001, SCYA21, UNQ784/PRO1600 / Production host: Escherichia coli (E. coli) / References: UniProt: O00585

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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: 0.500 mM [U-100% 13C; U-100% 15N] CCL21/SLC/6Ckine/Exodus-2, 10 % D2O, 25 mM [U-2H] MES, 0.02 % sodium azide, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.500 mMCCL21/SLC/6Ckine/Exodus-2-1[U-100% 13C; U-100% 15N]1
10 %D2O-21
25 mMMES-3[U-2H]1
0.02 %sodium azide-41
Sample conditionsIonic strength: 21 mM / pH: 6.1 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMRBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: 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: CCL21 STRUCTURES ARE BASED ON A TOTAL OF 743 NOE CONSTRAINTS (355 INTRA, 170 SEQUENTIAL, 64 MEDIUM, 154 LONG RANGE AND 90 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS)
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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