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- PDB-1u4r: Crystal Structure of human RANTES mutant 44-AANA-47 -

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Basic information

Entry
Database: PDB / ID: 1u4r
TitleCrystal Structure of human RANTES mutant 44-AANA-47
ComponentsSmall inducible cytokine A5
KeywordsATTRACTANT / CHEMOATTRACTANT / CYTOKINE / CHEMOKINE / RANTES / MUTANT / GLYCOSAMINOGLYCAN / PROTEIN-HEPARIN DISACCHARIDE COMPLEX
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 / host-mediated suppression 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShaw, J.P. / Johnson, Z. / Borlat, F. / Zwahlen, C. / Kungl, A. / Roulin, K. / Harrenga, A. / Wells, T.N.C. / Proudfoot, A.E.I.
CitationJournal: Structure / Year: 2004
Title: The X-ray structure of RANTES: heparin-derived disaccharides allows the rational design of chemokine inhibitors.
Authors: Shaw, J.P. / Johnson, Z. / Borlat, F. / Zwahlen, C. / Kungl, A. / Roulin, K. / Harrenga, A. / Wells, T.N. / Proudfoot, A.E.
History
DepositionJul 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small inducible cytokine A5
B: Small inducible cytokine A5
C: Small inducible cytokine A5
D: Small inducible cytokine A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8157
Polymers30,5274
Non-polymers2883
Water3,477193
1
A: Small inducible cytokine A5
B: Small inducible cytokine A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4554
Polymers15,2632
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-44 kcal/mol
Surface area7650 Å2
MethodPISA
2
C: Small inducible cytokine A5
D: Small inducible cytokine A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3593
Polymers15,2632
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-27 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.818, 80.475, 65.442
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Small inducible cytokine A5 / CCL5 / T-cell specific RANTES protein / SIS-delta / T cell-specific protein P228 / TCP228


Mass: 7631.676 Da / Num. of mol.: 4 / Mutation: R44A, K45A, R47A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, SCYA5 / Plasmid: pET23d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13501
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 400, 100mM acetate buffer, 200mM (NH4)2SO4, 10% (v/v) glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 12, 2002 / Details: mirrors
RadiationMonochromator: Osmic MaxFlux Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 11304 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / Num. unique all: 917 / % possible all: 75

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Processing

Software
NameVersionClassification
CNX2002refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1u4p

1u4p


Resolution: 2.2→15.63 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 957758.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1166 10.3 %RANDOM
Rwork0.222 ---
all-12435 --
obs-11269 93.8 %-
Solvent computationSolvent model: BABINET / Bsol: 280 Å2
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.88 Å20 Å2-6.4 Å2
2---7.5 Å20 Å2
3---11.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→15.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 15 193 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_scangle_it2.092.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 149 9.5 %
Rwork0.274 1427 -
obs-1576 78.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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