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- PDB-1s4j: NMR structure of cross-reactive peptides from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 1s4j
TitleNMR structure of cross-reactive peptides from Homo sapiens
Components60S acidic ribosomal protein P2
KeywordsRIBOSOME / antigenic peptide / ribosomal p2 protein / Chagas disease
Function / homology
Function and homology information


cytoplasmic translational elongation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit ...cytoplasmic translational elongation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Regulation of expression of SLITs and ROBOs / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / focal adhesion / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein
Similarity search - Domain/homology
Large ribosomal subunit protein P2
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSoares, M.R. / Bisch, P.M. / Campos de Carvalho, A.C. / Valente, A.P. / Almeida, F.C.L.
CitationJournal: Febs Lett. / Year: 2004
Title: Correlation between conformation and antibody binding: NMR structure of cross-reactive peptides from T. cruzi, human and L. braziliensis
Authors: Soares, M.R. / Bisch, P.M. / Campos De Carvalho, A.C. / Valente, A.P. / Almeida, F.C.L.
History
DepositionJan 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 60S acidic ribosomal protein P2


Theoretical massNumber of molelcules
Total (without water)1,4761
Polymers1,4761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 60S acidic ribosomal protein P2 / Ribosomal P2 protein


Mass: 1476.477 Da / Num. of mol.: 1 / Fragment: h13 - C-terminal domain / Source method: obtained synthetically
Details: peptide obtained by solid phase synthesis. the sequence is naturally found in Homo sapiens
References: UniProt: P05387

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM of peptide; 10% D2O; 10mM phosphate buffer at pH 5.5
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM phosphate buffer / pH: 5.5 / Pressure: ambient / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX4002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
NMRView5.03Bruce A. Johnsondata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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