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- PDB-6stk: Crystal structure of the CC-chemokine 5 (CCL5) E66S mutation -

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Basic information

Entry
Database: PDB / ID: 6stk
TitleCrystal structure of the CC-chemokine 5 (CCL5) E66S mutation
ComponentsC-C motif chemokine 5
KeywordsIMMUNE SYSTEM / CC-CHEMOKINE
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / activation of phospholipase D activity / chemokine receptor antagonist activity / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / receptor signaling protein tyrosine kinase activator activity ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / activation of phospholipase D activity / chemokine receptor antagonist activity / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of receptor signaling pathway via STAT / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of homotypic cell-cell adhesion / neutrophil activation / positive regulation of G protein-coupled receptor signaling pathway / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / negative regulation of T cell apoptotic process / chemokine-mediated signaling pathway / positive regulation of T cell apoptotic process / eosinophil chemotaxis / positive regulation of calcium ion transport / positive regulation of monocyte chemotaxis / positive regulation of innate immune response / cell surface receptor signaling pathway via STAT / chemokine activity / regulation of T cell activation / Chemokine receptors bind chemokines / dendritic cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / leukocyte cell-cell adhesion / phospholipase activator activity / negative regulation of viral genome replication / positive regulation of smooth muscle cell migration / Interleukin-10 signaling / positive regulation of macrophage chemotaxis / chemoattractant activity / macrophage chemotaxis / exocytosis / monocyte chemotaxis / positive regulation of translational initiation / cellular response to interleukin-1 / cellular response to fibroblast growth factor stimulus / negative regulation by host of viral transcription / positive regulation of TOR signaling / positive regulation of T cell migration / positive regulation of viral genome replication / positive regulation of T cell proliferation / positive regulation of cell adhesion / regulation of insulin secretion / positive regulation of epithelial cell proliferation / epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / response to virus / cellular response to virus / cellular response to type II interferon / response to toxic substance / intracellular calcium ion homeostasis / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / calcium ion transport / cellular response to tumor necrosis factor / cell-cell signaling / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / 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
Similarity search - Domain/homology
ACETATE ION / C-C motif chemokine 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsRamirez-Escudero, M. / Janssen, B.J.C.
Funding support1items
OrganizationGrant numberCountry
European Research Council677500
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural characterization of anti-CCL5 activity of the tick salivary protein evasin-4.
Authors: Denisov, S.S. / Ramirez-Escudero, M. / Heinzmann, A.C.A. / Ippel, J.H. / Dawson, P.E. / Koenen, R.R. / Hackeng, T.M. / Janssen, B.J.C. / Dijkgraaf, I.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7914
Polymers15,6402
Non-polymers1512
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-11 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.916, 56.324, 94.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 26 through 89 or resid 124))
21(chain B and (resid 26 through 89 or resid 201))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 26 through 89 or resid 124))A0
211(chain B and (resid 26 through 89 or resid 201))B0

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Components

#1: Protein C-C motif chemokine 5 / 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: 7819.975 Da / Num. of mol.: 2 / Mutation: E66S
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% glycerol, 25.5% PEG 4000, 85mM acetate buffer pH 4.6, 0.17 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.52→48.31 Å / Num. obs: 20411 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.8
Reflection shellResolution: 1.52→1.55 Å / Rmerge(I) obs: 0.143 / Num. unique obs: 972 / CC1/2: 0.679

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5coy

5coy


Resolution: 1.52→48.31 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.2028 1026 5.04 %
Rwork0.1804 --
obs0.1816 20346 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.26 Å2 / Biso mean: 30.9706 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 1.52→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 10 136 1194
Biso mean--59.21 38.15 -
Num. residues----129
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A627X-RAY DIFFRACTION12.163TORSIONAL
12B627X-RAY DIFFRACTION12.163TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.52-1.60010.29691360.25452728
1.6001-1.70040.27781470.22772690
1.7004-1.83170.21961510.1882703
1.8317-2.0160.22391350.17672733
2.016-2.30770.20511450.16972743
2.3077-2.90720.19611530.18772789
2.9072-36.070.1861590.16972934
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.21620.38450.47124.86522.06392.29250.03730.027-0.0365-0.2279-0.05970.0728-0.02270.04830.01380.18250.00760.00260.15080.00450.14870.8914-15.375-21.8316
21.94620.37260.85521.714-0.09747.4178-0.0541-0.02740.01210.1545-0.0625-0.1095-0.11310.20360.08720.1677-0.0025-0.00230.14070.0050.172110.3921-4.4193-1.1522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 3:104)A3 - 104
2X-RAY DIFFRACTION2(chain B and resseq 3:101)B3 - 101

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