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- PDB-8ong: Structure of the endothelial monocyte activating polypeptide II (... -

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Basic information

Entry
Database: PDB / ID: 8ong
TitleStructure of the endothelial monocyte activating polypeptide II (EMAP II) in solution
ComponentsAminoacyl tRNA synthase complex-interacting multifunctional protein 1
KeywordsCYTOKINE / cytokines / EMAP II / NMR spectroscopy / molecular dynamic simulations
Function / homology
Function and homology information


positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / cytokine activity / GTPase binding / cell-cell signaling / angiogenesis ...positive regulation of glucagon secretion / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / leukocyte migration / negative regulation of endothelial cell proliferation / cytokine activity / GTPase binding / cell-cell signaling / angiogenesis / defense response to virus / 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, OB-fold
Similarity search - Domain/homology
Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SOLUTION SCATTERING / molecular dynamics
AuthorsLozhko, D. / Kolomiiets, L. / Kornelyuk, A.I. / Zhukov, I.
Funding support Poland, European Union, 2items
OrganizationGrant numberCountry
Polish National Science CentreN 30107131/2150 Poland
European Communitys Seventh Framework ProgrammeBioNMR contract 261863European Union
CitationJournal: To Be Published
Title: Structural analysis and conformational flexibility of endothelial monocyte activating polypeptide II (EMAP II) by means NMR spectroscopy and molecular dynamics simulations
Authors: Lozhko, D. / Kolomiiets, L. / Zhukova, L. / Taube, M. / Dadlez, M. / Kozak, M. / Kornelyuk, A.I. / Zhukov, I.
History
DepositionApr 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoacyl tRNA synthase complex-interacting multifunctional protein 1


Theoretical massNumber of molelcules
Total (without water)18,5601
Polymers18,5601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 / Multisynthase complex auxiliary component p43


Mass: 18559.541 Da / Num. of mol.: 1 / Mutation: N-terminal AMD after cleavage of the HisTag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP1, EMAP2, SCYE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12904

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HN(CO)CA
141isotropic13D HNCA
151isotropic13D CBCA(CO)NH
161isotropic13D HN(CA)CB
171isotropic34D HN(CO)CA NUS
181isotropic34D HN(CA)CO NUS
191isotropic34D (H)CCH-TOCSY
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D C(CO)NH
1131isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-13C; U-15N] EMAP II, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.4 mM [U-15N] EMAP II, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMEMAP II[U-13C; U-15N]1
0.4 mMEMAP II[U-15N]2
Sample conditionsDetails: PBS 50 mM, NaCl 250 mM, DTT 10 mM. / Ionic strength: 50 mM / Ionic strength err: 2 / Label: conditions_1 / pH: 8.0 / PH err: 0.2 / Pressure: 1 bar / Temperature: 298 K / Temperature err: 0.2

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent VNMRSAgilentVNMRS8001
Agilent VNMRSAgilentVNMRS7003
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
VnmrJAgilent Inc.collection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee W, Tonelli M & Markley JLchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAKrieger E, KoraimannG & VriendGrefinement
NMRFAM-SPARKYLee W, Tonelli M & Markley JLpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: molecular dynamic in water box
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 19

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