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- PDB-2w1o: NMR structure of dimerization domain of human ribosomal protein P2 -

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Basic information

Entry
Database: PDB / ID: 2w1o
TitleNMR structure of dimerization domain of human ribosomal protein P2
Components60S ACIDIC RIBOSOMAL PROTEIN P2
KeywordsTRANSLATION / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / RIBOSOME / DIMERIZATION / PHOSPHOPROTEIN
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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression ...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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / focal adhesion / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #1410 / Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Large ribosomal subunit protein P2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA
AuthorsLee, K.M. / Chan, D.S. / Sze, K.H. / Zhu, G. / Shaw, P.C. / Wong, K.B.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Solution Structure of the Dimerization Domain of Ribosomal Protein P2 Provides Insights for the Structural Organization of Eukaryotic Stalk.
Authors: Lee, K.M. / Yu, C.W. / Chan, D.S. / Chiu, T.Y. / Zhu, G. / Sze, K.H. / Shaw, P.C. / Wong, K.B.
History
DepositionOct 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 60S ACIDIC RIBOSOMAL PROTEIN P2
B: 60S ACIDIC RIBOSOMAL PROTEIN P2


Theoretical massNumber of molelcules
Total (without water)14,4142
Polymers14,4142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area6990 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200LEAST RESTRAINT VIOLATION
RepresentativeModel #7

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Components

#1: Protein 60S ACIDIC RIBOSOMAL PROTEIN P2 / RENAL CARCINOMA ANTIGEN NY-REN-44 / HUMAN RIBOSOME PROTEIN P2


Mass: 7207.184 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P05387
Sequence detailsTHE SUBMITTED SEQUENCE CONTAINS THE N-TERMINAL DIMERIZATION DOMAIN (RESIDUE 1-69) OF HUMAN P2, AND ...THE SUBMITTED SEQUENCE CONTAINS THE N-TERMINAL DIMERIZATION DOMAIN (RESIDUE 1-69) OF HUMAN P2, AND AN EXTRA N-TERMINAL ALA RESIDUE AS A CLONING ARTEFACT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER / 10% D2O
Sample conditionsIonic strength: 200MM SODIUM SULFATE / pH: 7.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 200 / Conformers submitted total number: 10

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