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- PDB-2rrs: NMR Structure of LC4 transmembrane segment of CCR5 -

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Basic information

Entry
Database: PDB / ID: 2rrs
TitleNMR Structure of LC4 transmembrane segment of CCR5
ComponentsC-C chemokine receptor type 5
KeywordsSIGNALING PROTEIN / LC4 / CCR5 / HIV / transmembrane protein / GPCR
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / cell chemotaxis / calcium-mediated signaling / calcium ion transport / chemotaxis / MAPK cascade / virus receptor activity / cell-cell signaling / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / endosome / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 5 / Chemokine receptor family / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsMiyamoto, K.
CitationJournal: Plos One / Year: 2011
Title: Solution Structure of LC4 Transmembrane Segment of CCR5
Authors: Miyamoto, K. / Togiya, K.
History
DepositionApr 11, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C chemokine receptor type 5


Theoretical massNumber of molelcules
Total (without water)1,9651
Polymers1,9651
Non-polymers00
Water0
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 C-C chemokine receptor type 5 / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 1965.297 Da / Num. of mol.: 1 / Fragment: LC4 transmembrane segment, UNP residues 157-174 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 2 mM LC4-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: LC4-1
Sample conditionsIonic strength: 280 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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