[English] 日本語
Yorodumi
- PDB-2mlo: Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a Membr... -

+
Open data


ID or keywords:

Loading...

-
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 / CCR2 chemokine receptor binding / negative regulation of type 2 immune response / regulation of vascular endothelial growth factor production / 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 / fibrillar center / cytokine-mediated signaling pathway / 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 / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more