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- PDB-2mzx: CCR5-ECL2 helical structure, residues Q186-T195 -

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Basic information

Entry
Database: PDB / ID: 2mzx
TitleCCR5-ECL2 helical structure, residues Q186-T195
ComponentsC-C chemokine receptor type 5
KeywordsSIGNALING PROTEIN
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 / chemotaxis / calcium ion transport / 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 / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsAbayev, M. / Anglister, J.
CitationJournal: Febs J. / Year: 2015
Title: An extended CCR5 ECL2 peptide forms a helix that binds HIV-1 gp120 through non-specific hydrophobic interactions.
Authors: Abayev, M. / Moseri, A. / Tchaicheeyan, O. / Kessler, N. / Arshava, B. / Naider, F. / Scherf, T. / Anglister, J.
History
DepositionFeb 26, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: C-C chemokine receptor type 5


Theoretical massNumber of molelcules
Total (without water)1,3911
Polymers1,3911
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)11 / 74structures with the lowest energy
RepresentativeModel #1minimized average structure

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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: 1390.519 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 186-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCR5, CMKBR5 / Production host: Escherichia coli (E. coli) / References: UniProt: P51681

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: CCR5 ECL2 peptides inhibit HIV-1 infection. The structure of an elongated ECL2 peptide was determined using triple resonance approach by NMR. A helical structure was found at the C-terminal ...Details: CCR5 ECL2 peptides inhibit HIV-1 infection. The structure of an elongated ECL2 peptide was determined using triple resonance approach by NMR. A helical structure was found at the C-terminal segment of this peptide, residues Q186-T195.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCA
1413D HN(CO)CA
1512D 1H-15N HSQC
1612D 1H-1H NOESY
1713D 1H-15N NOESY
1812D 1H-1H TOCSY
1913D HNCO

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Sample preparation

DetailsContents: 20 mM [U-99% 2H] acetic acid, 0.005 % v/v Thiomersal, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMacetic acid-1[U-99% 2H]1
0.005 v/vThiomersal-21
Sample conditionsIonic strength: 0 / pH: 4.8 / Pressure: ambient / Temperature: 277 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.31Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.31Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 307 / NOE intraresidue total count: 131 / NOE medium range total count: 68 / NOE sequential total count: 108 / Protein phi angle constraints total count: 12 / Protein psi angle constraints total count: 10
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 74 / Conformers submitted total number: 11 / Maximum upper distance constraint violation: 0.5 Å / Torsion angle constraint violation method: TALOS-N
NMR ensemble rmsDistance rms dev: 0.57 Å / Distance rms dev error: 0.25 Å

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