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- PDB-1eqt: MET-RANTES -

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Basic information

Entry
Database: PDB / ID: 1eqt
TitleMET-RANTES
ComponentsT-CELL SPECIFIC RANTES PROTEIN
KeywordsCYTOKINE / CHEMOATTRACTANT / RANTES
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 / 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: 1.6 Å
AuthorsHoover, D.M. / Shaw, J. / Gryczynski, Z. / Proudfoot, A.E.I. / Wells, T.
Citation
Journal: PROTEIN PEPT.LETT. / Year: 2000
Title: The Crystal Structure of MET-RANTES: Comparison with Native RANTES and AOP-RANTES
Authors: Hoover, D.M. / Shaw, J. / Gryczynski, Z. / Proudfoot, A.E.I. / Wells, T.
#1: Journal: Chem.Biol. / Year: 1999
Title: Total Chemical Synthesis and High-resolution Crystal Structure of the Potent anti-HIV Protein AOP-RANTES
Authors: Wilken, J. / Hoover, D. / Thompson, D.A. / Barlow, P.N. / McSparron, H. / Picard, L. / Wlodawer, A. / Lubkowski, J. / Kent, S.B.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Extension of Recombinant Human RANTES by the Retention of the Initiating Methionine Produces a Potent Antagonist
Authors: Proudfoot, A.E. / Power, C.A. / Hoogewerf, A.J. / Montjovent, M.O. / Borlat, F. / Offord, R.E. / Wells, T.N.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.4Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: T-CELL SPECIFIC RANTES PROTEIN
B: T-CELL SPECIFIC RANTES PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9604
Polymers15,7682
Non-polymers1922
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.019, 56.809, 93.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is likely a dimer constructed of both chain A and B.

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Components

#1: Protein T-CELL SPECIFIC RANTES PROTEIN / SMALL INDUCIBLE CYTOKINE A5


Mass: 7884.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsINITIATING MET RETAINED.

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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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 35000, ammonium sulfate, sodium succinate, MES, sodium acetate, ethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: other / Details: Wilken, J., (1999) Chem.Biol., 6, 43.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMsodium acetate11
215 mg/mlprotein11
30.1 Mammonium sulfate11
4225 mMsodium succinate11
5275 mMMES11
615 %ethanol11
70.1 Mammonium sulfate12
8225 mMsodium succinate12
9275 mMMES12
1015 %ethanol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 23, 1998 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 44155 / Num. obs: 17136 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1650 / % possible all: 96
Reflection
*PLUS
Num. measured all: 44155

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RANTES (NMR MODEL 1RTN)

1rtn


Resolution: 1.6→20 Å / Num. parameters: 513 / Num. restraintsaints: 451 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1655 10 %RANDOM
Rwork0.1868 ---
all0.178 17136 --
obs0.178 16548 84.2 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1281
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 10 187 1281
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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