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- PDB-6log: Crystal structure of human CCL5-12AAA14 mutant -

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Basic information

Entry
Database: PDB / ID: 6log
TitleCrystal structure of human CCL5-12AAA14 mutant
ComponentsC-C motif chemokine 5Chemokine
KeywordsCYTOKINE / CCL5 / RANTES / chemokine / dimer / CCL5 mutant / sulfate binding
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: 2.55 Å
AuthorsChen, Y.C. / Li, J.Y. / Huang, C.H. / Sue, S.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2113-M-007-003 Taiwan
CitationJournal: Int J Mol Sci / Year: 2020
Title: N-terminal Backbone Pairing Shifts in CCL5- 12 AAA 14 Dimer Interface: Structural Significance of the FAY Sequence.
Authors: Li, J.Y. / Chen, Y.C. / Lee, Y.Z. / Huang, C.H. / Sue, S.C.
History
DepositionJan 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 5


Theoretical massNumber of molelcules
Total (without water)7,8251
Polymers7,8251
Non-polymers00
Water1267
1
A: C-C motif chemokine 5

A: C-C motif chemokine 5


Theoretical massNumber of molelcules
Total (without water)15,6502
Polymers15,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1150 Å2
ΔGint-6 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.329, 48.329, 60.401
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

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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: 7825.015 Da / Num. of mol.: 1 / Mutation: F12A, Y14A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2M Magnesium acetate tetrahydrate pH 7.9, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.44→30 Å / Num. obs: 3262 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.954 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.036 / Rrim(I) all: 0.078 / Net I/σ(I): 20.2
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 315 / CC1/2: 0.816 / Rpim(I) all: 0.367 / Rrim(I) all: 0.861

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EQT

1eqt


Resolution: 2.55→18.88 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 26.109 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.466 / ESU R Free: 0.276
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 103 3.6 %RANDOM
Rwork0.2141 ---
obs0.2153 2749 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.36 Å2 / Biso mean: 83.06 Å2 / Biso min: 50.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å20 Å2
2--1.2 Å20 Å2
3----3.88 Å2
Refinement stepCycle: final / Resolution: 2.55→18.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms501 0 0 7 508
Biso mean---82 -
Num. residues----63
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013515
X-RAY DIFFRACTIONr_bond_other_d0.0010.017478
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.673700
X-RAY DIFFRACTIONr_angle_other_deg1.2911.5781110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.139562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1312027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.4251587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.716155
X-RAY DIFFRACTIONr_chiral_restr0.0750.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02571
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02112
LS refinement shellResolution: 2.55→2.613 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.447 8 -
Rwork0.323 180 -
obs--98.95 %
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)
110.2831-0.2747-1.06536.1230.1555.95560.055-0.45130.56110.13650.0485-0.3424-0.90870.4898-0.10350.2074-0.0626-0.03220.0544-0.03350.06643.53814.649.127
24.95213.8149-1.03572.941-0.82390.5345-0.2375-0.3810.1002-0.1713-0.27350.0342-0.1184-0.09750.5110.50870.2505-0.25170.1758-0.29010.87891.19611.579.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 68
2X-RAY DIFFRACTION2A101 - 107

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