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- PDB-2jyo: NMR Solution structure of Human MIP-3alpha/CCL20 -

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Basic information

Entry
Database: PDB / ID: 2jyo
TitleNMR Solution structure of Human MIP-3alpha/CCL20
ComponentsC-C motif chemokine 20 (Small-inducible cytokine A20) (Macrophage inflammatory protein 3 alpha) (MIP-3-alpha) (Liver and activation-regulated chemokine) (CC chemokine LARC) (Beta chemokine exodus-1)
KeywordsCYTOKINE / Protein / Chemokine / Alternative splicing / Antibiotic / Antimicrobial / Chemotaxis / Inflammatory response / Polymorphism / Secreted
Function / homology
Function and homology information


thymocyte migration / CCR6 chemokine receptor binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / positive regulation of T cell migration / T cell migration / cell chemotaxis ...thymocyte migration / CCR6 chemokine receptor binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / positive regulation of T cell migration / T cell migration / cell chemotaxis / calcium-mediated signaling / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / G alpha (i) signalling events / defense response to bacterium / positive regulation of cell migration / inflammatory response / immune response / signal transduction / 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 20
Similarity search - Component
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsChan, D.I. / Hunter, H.N. / Tack, B.F. / Vogel, H.J.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2008
Title: Human macrophage inflammatory protein 3alpha: protein and peptide nuclear magnetic resonance solution structures, dimerization, dynamics, and anti-infective properties.
Authors: Chan, D.I. / Hunter, H.N. / Tack, B.F. / Vogel, H.J.
History
DepositionDec 14, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 20 (Small-inducible cytokine A20) (Macrophage inflammatory protein 3 alpha) (MIP-3-alpha) (Liver and activation-regulated chemokine) (CC chemokine LARC) (Beta chemokine exodus-1)


Theoretical massNumber of molelcules
Total (without water)8,0441
Polymers8,0441
Non-polymers00
Water00
1


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

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Components

#1: Protein C-C motif chemokine 20 (Small-inducible cytokine A20) (Macrophage inflammatory protein 3 alpha) (MIP-3-alpha) (Liver and activation-regulated chemokine) (CC chemokine LARC) (Beta chemokine exodus-1)


Mass: 8043.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P78556
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
1422D 1H-1H NOESY
1522D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM Protein, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM Protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.9 mMProtein1
0.9 mMProtein2
Sample conditionspH: 4.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
ARIALinge, J.P. et al.structure solution
CNS1.1Brunger, A.T. et al.refinement
NMRView5.0.4Johnson, B. et al.data analysis
XwinNMR3.0, 3.5Bruker Biospincollection
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: In total, 2362 restraints were used: 1827 unambiguous NOE restraints, 455 ambiguous restraints, 64 broad dihedral restraints and 16 hydrogen bonding restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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