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- PDB-5yam: Solution structure of mice Met-CCL5/RANTES -

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Basic information

Entry
Database: PDB / ID: 5yam
TitleSolution structure of mice Met-CCL5/RANTES
ComponentsC-C motif chemokine 5
KeywordsCYTOKINE / inflammatory / heparin / dimer / antagonist / chemokine
Function / homology
Function and homology information


T-helper 1 cell diapedesis / : / Chemokine receptors bind chemokines / pseudopodium assembly / chemokine receptor antagonist activity / : / activation of phospholipase D activity / : / : / positive regulation of cellular biosynthetic process ...T-helper 1 cell diapedesis / : / Chemokine receptors bind chemokines / pseudopodium assembly / chemokine receptor antagonist activity / : / activation of phospholipase D activity / : / : / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of mast cell chemotaxis / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / G alpha (i) signalling events / positive regulation of T cell chemotaxis / positive regulation of homotypic cell-cell adhesion / negative regulation of G protein-coupled receptor signaling pathway / CCR chemokine receptor binding / lymphocyte chemotaxis / phosphatidylinositol phospholipase C activity / positive regulation of fever generation / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / neutrophil activation / positive regulation of calcium ion transport / eosinophil chemotaxis / positive regulation of osteoclast differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / chemokine activity / regulation of T cell activation / leukocyte cell-cell adhesion / negative regulation of viral genome replication / phospholipase activator activity / positive regulation of macrophage chemotaxis / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / response to type II interferon / monocyte chemotaxis / regulation of insulin secretion / cellular response to organic cyclic compound / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / cellular response to interleukin-1 / response to tumor necrosis factor / positive regulation of T cell proliferation / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / positive regulation of neuron differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neutrophil chemotaxis / positive regulation of GTPase activity / response to cytokine / positive regulation of epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / : / MAPK cascade / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / positive regulation of gene expression / protein homodimerization activity / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, Y.-C. / Chen, S.-P. / Lee, Y.-Z. / Sue, S.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
MOST106-2113-M-007 -020 Taiwan
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Integrative Model to Coordinate the Oligomerization and Aggregation Mechanisms of CCL5.
Authors: Chen, Y.C. / Chen, S.P. / Li, J.Y. / Chen, P.C. / Lee, Y.Z. / Li, K.M. / Zarivach, R. / Sun, Y.J. / Sue, S.C.
History
DepositionSep 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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 motif chemokine 5
B: C-C motif chemokine 5


Theoretical massNumber of molelcules
Total (without water)16,0322
Polymers16,0322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1040 Å2
ΔGint-9 kcal/mol
Surface area10150 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein C-C motif chemokine 5 / MuRantes / SIS-delta / Small-inducible cytokine A5 / T-cell-specific protein RANTES


Mass: 8016.196 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ccl5, Scya5
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
Strain (production host): BL21(DE3) / References: UniProt: P30882

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D HN(CO)CA
161isotropic13D HN(COCA)CB
1121isotropic13D HBHA(CO)NH
1111isotropic13D H(CCO)NH
1101isotropic13D C(CO)NH
191isotropic23D (H)CCH-TOCSY
181isotropic23D (H)CCH-COSY
171isotropic22D 1H-13C HSQC aromatic
1131isotropic23D 1H-15N NOESY
1141isotropic23D 1H-13C NOESY aliphatic
1151isotropic23D 1H-13C NOESY aromatic
1161isotropic22D (HB)CB(CGCD)HD
1171isotropic22D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-13C; U-15N] C-C motif chemokine 5, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 200 uM / Component: C-C motif chemokine 5 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 3.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin3.5Bruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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