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- PDB-5cmd: Oligomer crystal structure of CC chemokine 5 (CCL5) -

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Basic information

Entry
Database: PDB / ID: 5cmd
TitleOligomer crystal structure of CC chemokine 5 (CCL5)
ComponentsC-C motif chemokine 5Chemokine
KeywordsCYTOKINE / CC chemokine / high oligomer
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / 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 ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / 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 / positive regulation of activation of Janus kinase activity / receptor signaling protein tyrosine kinase activator activity / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / CCR chemokine receptor binding / lymphocyte chemotaxis / neutrophil activation / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / positive regulation of calcium ion transport / eosinophil chemotaxis / positive regulation of innate immune response / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / regulation of T cell activation / leukocyte cell-cell adhesion / positive regulation of macrophage chemotaxis / negative regulation of viral genome replication / phospholipase activator activity / macrophage chemotaxis / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of translational initiation / regulation of insulin secretion / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / positive regulation of viral genome replication / cellular response to interleukin-1 / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / neutrophil chemotaxis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / intracellular calcium ion homeostasis / response to toxic substance / cellular response to virus / cellular response to type II interferon / : / calcium ion transport / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein homodimerization activity / extracellular space / extracellular region / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.086 Å
AuthorsLiang, W.G. / Tang, W.-J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM81539 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3.
Authors: Liang, W.G. / Triandafillou, C.G. / Huang, T.Y. / Zulueta, M.M. / Banerjee, S. / Dinner, A.R. / Hung, S.C. / Tang, W.J.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: C-C motif chemokine 5
D: C-C motif chemokine 5
E: C-C motif chemokine 5
F: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,14517
Polymers45,0886
Non-polymers1,05711
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-124 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.720, 124.720, 127.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
C-C motif chemokine 5 / Chemokine / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES


Mass: 7514.645 Da / Num. of mol.: 6 / Fragment: unp residues 27-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.33 Å3/Da / Density % sol: 80.56 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris, 1.8 M Ammonium sulfate / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 20688 / % possible obs: 99.9 % / Observed criterion σ(F): 3.28 / Observed criterion σ(I): 3.28 / Redundancy: 7.4 % / Rmerge(I) obs: 0.146 / Rsym value: 0.097 / Net I/σ(I): 29
Reflection shellResolution: 3.05→3.11 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 3.28 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5COY

5coy


Resolution: 3.086→40.824 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 2003 9.7 %
Rwork0.213 --
obs0.2173 20654 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.086→40.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 55 0 3163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043272
X-RAY DIFFRACTIONf_angle_d0.8514426
X-RAY DIFFRACTIONf_dihedral_angle_d14.7511204
X-RAY DIFFRACTIONf_chiral_restr0.032461
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0864-3.16360.40571470.34681301X-RAY DIFFRACTION100
3.1636-3.24910.38461440.29051341X-RAY DIFFRACTION100
3.2491-3.34470.31991400.30081329X-RAY DIFFRACTION100
3.3447-3.45260.32921420.26521316X-RAY DIFFRACTION100
3.4526-3.57590.31751470.26751333X-RAY DIFFRACTION100
3.5759-3.7190.25411360.24751333X-RAY DIFFRACTION100
3.719-3.88810.27991450.22681333X-RAY DIFFRACTION100
3.8881-4.09290.24121420.20971312X-RAY DIFFRACTION100
4.0929-4.34910.26241480.19061334X-RAY DIFFRACTION100
4.3491-4.68450.19391400.1731332X-RAY DIFFRACTION100
4.6845-5.1550.24941370.17791338X-RAY DIFFRACTION100
5.155-5.89910.22661450.18611345X-RAY DIFFRACTION100
5.8991-7.42490.26011420.22171346X-RAY DIFFRACTION100
7.4249-40.82780.24061480.20381358X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -44.3446 Å / Origin y: 26.03 Å / Origin z: -13.748 Å
111213212223313233
T0.8108 Å2-0.1157 Å20.0009 Å2-0.6995 Å2-0.0124 Å2--0.7932 Å2
L1.3533 °20.3355 °2-0.2792 °2-1.7204 °2-0.6523 °2--1.0998 °2
S-0.0211 Å °0.1866 Å °0.122 Å °0.12 Å °0.1522 Å °0.1896 Å °-0.0698 Å °-0.0592 Å °-0.1208 Å °
Refinement TLS groupSelection details: all

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