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- PDB-2rll: CCR5 Nt(7-15) -

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Basic information

Entry
Database: PDB / ID: 2rll
TitleCCR5 Nt(7-15)
Components9-mer from C-C chemokine receptor type 5
KeywordsMEMBRANE PROTEIN / HIV-1 coreceptor CCR5 N-terminus bound to gp120:CD4 / G-protein coupled receptor / Glycoprotein / Host-virus interaction / Membrane / Polymorphism / Sulfation / Transducer / Transmembrane
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
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsBewley, C.A. / Lam, S.N.
CitationJournal: Science / Year: 2007
Title: Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4
Authors: Huang, C.-C. / Lam, S.N. / Acharya, P. / Tang, M. / Xiang, S.-H. / Hussan, S.S. / Stanfield, R.L. / Robinson, J. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Bewley, C.A. / Kwong, P.D.
History
DepositionJul 21, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 9-mer from C-C chemokine receptor type 5


Theoretical massNumber of molelcules
Total (without water)1,3071
Polymers1,3071
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)1 / 30structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide 9-mer from C-C chemokine receptor type 5 / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / HIV-1 fusion coreceptor / CHEMR13 / CD195 antigen


Mass: 1307.361 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 7-15 / Source method: obtained synthetically
Details: This peptide was chemically synthesized by solid phase synthesis and purified by reverse phase HPLC.; This sequence occurs naturally in humans.
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-13C HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-1H COSY

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Sample preparation

DetailsContents: 800uM protein; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 800 uM / Component: protein
Sample conditionsIonic strength: 50mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 1

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