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- PDB-2mlo: Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a Membr... -

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Basic information

Entry
Database: PDB / ID: 2mlo
TitleHuman CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a Membrane bound form
ComponentsMCP-1 receptor
KeywordsSIGNALING PROTEIN / CCR2 / PRO-C
Function / homology
Function and homology information


T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / positive regulation of thymocyte migration ...T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / positive regulation of thymocyte migration / positive regulation of hematopoietic stem cell migration / monocyte extravasation / regulation of vascular endothelial growth factor production / CCR2 chemokine receptor binding / negative regulation of type 2 immune response / positive regulation of NMDA glutamate receptor activity / Beta defensins / macrophage migration / positive regulation of monocyte extravasation / regulation of macrophage migration / regulation of T cell cytokine production / chemokine receptor activity / neutrophil clearance / positive regulation of leukocyte tethering or rolling / inflammatory response to wounding / positive regulation of T-helper 1 type immune response / positive regulation of T cell chemotaxis / positive regulation of alpha-beta T cell proliferation / C-C chemokine receptor activity / C-C chemokine binding / negative regulation of adenylate cyclase activity / cellular homeostasis / positive regulation of monocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / dendritic cell chemotaxis / regulation of T cell differentiation / monocyte chemotaxis / Interleukin-10 signaling / cell surface receptor signaling pathway via JAK-STAT / hemopoiesis / humoral immune response / blood vessel remodeling / cellular defense response / homeostasis of number of cells within a tissue / sensory perception of pain / positive regulation of interleukin-2 production / negative regulation of angiogenesis / positive regulation of synaptic transmission, glutamatergic / cell chemotaxis / calcium-mediated signaling / cytokine-mediated signaling pathway / fibrillar center / response to wounding / positive regulation of inflammatory response / intracellular calcium ion homeostasis / positive regulation of type II interferon production / chemotaxis / positive regulation of tumor necrosis factor production / positive regulation of T cell activation / positive regulation of cold-induced thermogenesis / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / perikaryon / inflammatory response / immune response / external side of plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CC chemokine receptor 2 / Chemokine receptor family / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
C-C chemokine receptor type 2 / C-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsEsaki, K. / Yoshinaga, S. / Tsuji, T. / Toda, E. / Terashima, Y. / Saitoh, T. / Kohda, D. / Kohno, T. / Osawa, M. / Ueda, T. ...Esaki, K. / Yoshinaga, S. / Tsuji, T. / Toda, E. / Terashima, Y. / Saitoh, T. / Kohda, D. / Kohno, T. / Osawa, M. / Ueda, T. / Shimada, I. / Matsushima, K. / Terasawa, H.
CitationJournal: Febs J. / Year: 2014
Title: Structural basis for the binding of the membrane-proximal C-terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT.
Authors: Esaki, K. / Yoshinaga, S. / Tsuji, T. / Toda, E. / Terashima, Y. / Saitoh, T. / Kohda, D. / Kohno, T. / Osawa, M. / Ueda, T. / Shimada, I. / Matsushima, K. / Terasawa, H.
History
DepositionMar 4, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Aug 24, 2022Group: Data collection / Database references / Category: citation / database_2 / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MCP-1 receptor


Theoretical massNumber of molelcules
Total (without water)2,1341
Polymers2,1341
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/peptide MCP-1 receptor / CCR2 / CHEMOKINE_(C-C_MOTIF)_RECEPTOR_2


Mass: 2133.540 Da / Num. of mol.: 1 / Fragment: C-Terminal region, UNP residues 90-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCR2 / Production host: Escherichia Coli (E. coli) / References: UniProt: O95950, UniProt: P41597*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D HNHA
1323D 1H-13C NOESY
1433D CBCA(CO)NH
1533D HN(CA)CB
1633D HBHA(CO)NH
1723D (H)CCH-TOCSY
1812D 1H-15N HSQC
1922D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1200 uM [U-100% 15N] CCR2_Pro-C-1, 20 uM sodium phosphate-2, 50 uM sodium chloride-3, 10 mM [U-99% 2H] DPC-4, 5 % [U-100% 2H] D2O-5, 95 % H2O-695% H2O/5% D2O
2200 uM [U-100% 13C; U-100% 15N] CCR2_Pro-C-7, 20 uM sodium phosphate-8, 50 uM sodium chloride-9, 10 mM [U-99% 2H] DPC-10, 100 % [U-100% 2H] D2O-11100% D2O
3200 uM [U-100% 13C; U-100% 15N] CCR2_Pro-C-12, 20 uM sodium phosphate-13, 50 uM sodium chloride-14, 10 mM [U-99% 2H] DPC-15, 5 % [U-100% 2H] D2O-16, 95 % H2O-1795% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMCCR2_Pro-C-1[U-100% 15N]1
20 uMsodium phosphate-21
50 uMsodium chloride-31
10 mMDPC-4[U-99% 2H]1
5 %D2O-5[U-100% 2H]1
95 %H2O-61
200 uMCCR2_Pro-C-7[U-100% 13C; U-100% 15N]2
20 uMsodium phosphate-82
50 uMsodium chloride-92
10 mMDPC-10[U-99% 2H]2
100 %D2O-11[U-100% 2H]2
200 uMCCR2_Pro-C-12[U-100% 13C; U-100% 15N]3
20 uMsodium phosphate-133
50 uMsodium chloride-143
10 mMDPC-15[U-99% 2H]3
5 %D2O-16[U-100% 2H]3
95 %H2O-173
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCE IIIBrukerAVANCE III6001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGUNTERT, MUMENTHALERstructure solution
CYANAGUNTERT, MUMENTHALERrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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