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- PDB-6c6d: 20mer crystal structure of CC chemokine 5 (CCL5) -

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Basic information

Entry
Database: PDB / ID: 6c6d
Title20mer crystal structure of CC chemokine 5 (CCL5)
ComponentsC-C motif chemokine 5
KeywordsCYTOKINE / chemokine / CCL / oligomer
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
C-C motif chemokine 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.5 Å
AuthorsLiang, W.G. / Tang, W.J.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association17GRNT33400028 United States
CitationJournal: To Be Published
Title: 20mer crystal structure of CC chemokine 5 (CCL5)
Authors: Liang, W.G. / Tang, W.J.
History
DepositionJan 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
G: C-C motif chemokine 5
H: C-C motif chemokine 5
I: C-C motif chemokine 5
J: C-C motif chemokine 5
K: C-C motif chemokine 5
L: C-C motif chemokine 5
S: C-C motif chemokine 5
T: C-C motif chemokine 5
M: C-C motif chemokine 5
N: C-C motif chemokine 5
O: C-C motif chemokine 5
P: C-C motif chemokine 5
Q: C-C motif chemokine 5
R: C-C motif chemokine 5


Theoretical massNumber of molelcules
Total (without water)150,29320
Polymers150,29320
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38920 Å2
ΔGint-163 kcal/mol
Surface area62490 Å2
Unit cell
Length a, b, c (Å)119.866, 322.783, 157.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 7514.645 Da / Num. of mol.: 20 / 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
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: 5.07 Å3/Da / Density % sol: 75.73 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / Details: 10% (v/v) 2-propanol, 0.1M HEPES pH 7.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 5.5→50 Å / Num. obs: 10103 / % possible obs: 97.6 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.066 / Rrim(I) all: 0.213 / Rsym value: 0.13 / Net I/σ(I): 10
Reflection shellResolution: 5.5→5.59 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.6 / Num. unique obs: 393 / CC1/2: 0.972 / Rpim(I) all: 0.22 / Rrim(I) all: 0.64 / Rsym value: 0.29 / Χ2: 0.547 / % possible all: 77.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L2U

5l2u


Resolution: 5.5→48.114 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.57
RfactorNum. reflection% reflection
Rfree0.2858 684 6.98 %
Rwork0.2477 --
obs0.2502 9802 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.5→48.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10284 0 0 0 10284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310604
X-RAY DIFFRACTIONf_angle_d0.71814392
X-RAY DIFFRACTIONf_dihedral_angle_d7.3536476
X-RAY DIFFRACTIONf_chiral_restr0.0481524
X-RAY DIFFRACTIONf_plane_restr0.0061824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.5004-5.92440.44471240.35551608X-RAY DIFFRACTION86
5.9244-6.51930.39351400.32931833X-RAY DIFFRACTION97
6.5193-7.45960.35921360.28651854X-RAY DIFFRACTION98
7.4596-9.38690.26031410.20281904X-RAY DIFFRACTION99
9.3869-48.11620.2351430.2291919X-RAY DIFFRACTION96

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