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- PDB-2mpm: Structural Basis of Receptor Sulfotyrosine Recognition by a CC Ch... -

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Basic information

Entry
Database: PDB / ID: 2mpm
TitleStructural Basis of Receptor Sulfotyrosine Recognition by a CC Chemokine: the N-terminal Region of CCR3 Bound to CCL11/Eotaxin-1
Components
  • CCR3
  • Eotaxin
KeywordsCYTOKINE / Chemokine CCL11 / Chemokine Receptor CCR3 / Sulfopeptide
Function / homology
Function and homology information


response to interleukin-13 / CCR3 chemokine receptor binding / chronic inflammatory response / response to interleukin-4 / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway ...response to interleukin-13 / CCR3 chemokine receptor binding / chronic inflammatory response / response to interleukin-4 / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / branching involved in mammary gland duct morphogenesis / chemokine activity / positive regulation of actin filament polymerization / monocyte chemotaxis / cellular response to interleukin-1 / positive regulation of endothelial cell proliferation / cytoskeleton organization / ERK1 and ERK2 cascade / neutrophil chemotaxis / positive regulation of GTPase activity / actin filament organization / response to virus / response to radiation / negative regulation of neurogenesis / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of angiogenesis / chemotaxis / cellular response to tumor necrosis factor / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / learning or memory / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / cell adhesion / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signal transduction / extracellular space / extracellular region
Similarity search - Function
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
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsMillard, C.J. / Ludeman, J.P. / Canals, M. / Bridgford, J.L. / Hinds, M.G. / Clayton, D.J. / Christopoulos, A. / Payne, R.J. / Stone, M.J.
CitationJournal: Structure / Year: 2014
Title: Structural Basis of Receptor Sulfotyrosine Recognition by a CC Chemokine: The N-Terminal Region of CCR3 Bound to CCL11/Eotaxin-1.
Authors: Millard, C.J. / Ludeman, J.P. / Canals, M. / Bridgford, J.L. / Hinds, M.G. / Clayton, D.J. / Christopoulos, A. / Payne, R.J. / Stone, M.J.
History
DepositionMay 26, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eotaxin
B: CCR3


Theoretical massNumber of molelcules
Total (without water)10,3212
Polymers10,3212
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 / 64structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein Eotaxin / C-C motif chemokine 11 / Eosinophil chemotactic protein / Small-inducible cytokine A11


Mass: 8380.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL11, SCYA11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51671
#2: Protein/peptide CCR3


Mass: 1940.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Sulfopeptide / Source: (synth.) HOMO SAPIENS (human)
Source detailsEOTAXIN-1/CCL11 GROWN IN MINIMAL MEDIA FOR >99.8% INCORPORATION OF 13C AND 15N

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2212D 1H-13C HSQC
3312D 1H-13C HSQC aliphatic
4412D 1H-13C HSQC aromatic
5512D 1H-1H TOCSY
6612D 1H-1H NOESY
7713D CBCA(CO)NH
8813D C(CO)NH
9913D HN(CA)CB
101013D HBHA(CO)NH
111113D H(CCO)NH
121213D (H)CCH-TOCSY
131313D 1H-15N NOESY
141413D 1H-15N TOCSY
151513D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.2-0.4 MM [U-100% 13C, U-100% 15N] CCL11/EOTAXIN-1, 0.2-0.4 MM CCR3 SU1617 SULFOPEPTIDE, 95% V/V H2O, 5% V/V [U-100% 2H] D2O, 20 MM [U-100% 2H] SODIUM ACETATE-D6, 0.02% V/V SODIUM AZIDE, ...Contents: 0.2-0.4 MM [U-100% 13C, U-100% 15N] CCL11/EOTAXIN-1, 0.2-0.4 MM CCR3 SU1617 SULFOPEPTIDE, 95% V/V H2O, 5% V/V [U-100% 2H] D2O, 20 MM [U-100% 2H] SODIUM ACETATE-D6, 0.02% V/V SODIUM AZIDE, 20 UM DSS, 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCCL11/Eotaxin-1-1[U-100% 13C; U-100% 15N]0.2-0.41
mMCCR3 Su1617 sulfopeptide-20.2-0.41
95 %H2O-31
5 %D2O-4[U-100% 2H]1
20 mMsodium acetate-d6-5[U-100% 2H]1
0.02 %sodium azide-61
20 uMDSS-71
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: AMBIENT / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAvance2

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR_NIH 2.32, AQUA, PROCHECKNMRPROCHECKNMRSCHWIETERS, KUSZEWSKI, TJrefinement
TOPSPIN3.1structure solution
SPARKY3.92structure solution
CYANA2.1structure solution
CANDID2.1structure solution
TALOSstructure solution
X-PLOR_ NIH2.32structure solution
AQUAstructure solution
PROCHECKNMRstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1135 / NOE intraresidue total count: 276 / NOE long range total count: 368 / NOE medium range total count: 181 / NOE sequential total count: 255 / 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: 29 / Protein psi angle constraints total count: 29
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 64 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.019 Å / Distance rms dev error: 0.003 Å

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