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- PDB-1euj: A NOVEL ANTI-TUMOR CYTOKINE CONTAINS A RNA-BINDING MOTIF PRESENT ... -

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Basic information

Entry
Database: PDB / ID: 1euj
TitleA NOVEL ANTI-TUMOR CYTOKINE CONTAINS A RNA-BINDING MOTIF PRESENT IN AMINOACYL-TRNA SYNTHETASES
ComponentsENDOTHELIAL MONOCYTE ACTIVATING POLYPEPTIDE 2
KeywordsCYTOKINE / EMAP 2 / EMAP II / tRNA synthetase / apoptosis / RNA binding motif
Function / homology
Function and homology information


positive regulation of glucagon secretion / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / cell-cell signaling / GTPase binding ...positive regulation of glucagon secretion / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / leukocyte migration / negative regulation of endothelial cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / cell-cell signaling / GTPase binding / defense response to virus / angiogenesis / tRNA binding / inflammatory response / translation / apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / membrane / nucleus / cytosol
Similarity search - Function
: / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKim, Y. / Shin, J. / Li, R. / Cheong, C. / Kim, S.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: A novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases.
Authors: Kim, Y. / Shin, J. / Li, R. / Cheong, C. / Kim, K. / Kim, S.
History
DepositionApr 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ENDOTHELIAL MONOCYTE ACTIVATING POLYPEPTIDE 2
B: ENDOTHELIAL MONOCYTE ACTIVATING POLYPEPTIDE 2


Theoretical massNumber of molelcules
Total (without water)36,4842
Polymers36,4842
Non-polymers00
Water3,477193
1
A: ENDOTHELIAL MONOCYTE ACTIVATING POLYPEPTIDE 2


Theoretical massNumber of molelcules
Total (without water)18,2421
Polymers18,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDOTHELIAL MONOCYTE ACTIVATING POLYPEPTIDE 2


Theoretical massNumber of molelcules
Total (without water)18,2421
Polymers18,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.01, 38.34, 80.99
Angle α, β, γ (deg.)90, 112.90, 90
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer in vivo, but forms a dimer in a asymmetric unit in crystal by the two-fold.

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Components

#1: Protein ENDOTHELIAL MONOCYTE ACTIVATING POLYPEPTIDE 2 / EMAP 2


Mass: 18242.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q12904
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG 4000, 100 mM NaAcetate, 15 mM MgCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
30.5 mMbeta-mercaptoethanol1drop
41 mMEDTA1drop
5100 mM1dropKCl
6100 mMsodium acetate1reservoir
720 %(w/v)PEG40001reservoir
815 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 35728 / Num. obs: 31502 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.8 / Redundancy: 3.1 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.3
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.282 / % possible all: 37.9
Reflection
*PLUS
Num. measured all: 96335
Reflection shell
*PLUS
% possible obs: 37.9 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 2329 random
Rwork0.208 --
all0.213 31502 -
obs0.21 30829 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 0 193 2701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.58
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.7 Å2

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