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- PDB-2lbf: Solution structure of the dimerization domain of human ribosomal ... -

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Basic information

Entry
Database: PDB / ID: 2lbf
TitleSolution structure of the dimerization domain of human ribosomal protein P1/P2 heterodimer
Components
  • 60S acidic ribosomal protein P1
  • 60S acidic ribosomal protein P2
KeywordsRIBOSOMAL PROTEIN / ribosome / stalk / P1/P2
Function / homology
Function and homology information


cytoplasmic translational elongation / protein kinase activator activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translational elongation / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation ...cytoplasmic translational elongation / protein kinase activator activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translational elongation / 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) / ribonucleoprotein complex binding / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / focal adhesion / extracellular exosome / membrane / cytosol / cytoplasm
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 P1 / Large ribosomal subunit protein P2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsLee, K.-M. / Yu, C.W.-H. / Chiu, T.Y.-H. / Sze, K.-H. / Shaw, P.-C. / Wong, K.-B.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Solution structure of the dimerization domain of the eukaryotic stalk P1/P2 complex reveals the structural organization of eukaryotic stalk complex
Authors: Lee, K.-M. / Yu, C.W.-H. / Chiu, T.Y.-H. / Sze, K.-H. / Shaw, P.-C. / Wong, K.-B.
History
DepositionMar 30, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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 P1
B: 60S acidic ribosomal protein P2


Theoretical massNumber of molelcules
Total (without water)14,2952
Polymers14,2952
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)10 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein 60S acidic ribosomal protein P1


Mass: 7088.140 Da / Num. of mol.: 1 / Fragment: UNP residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPLP1, RRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05386
#2: Protein 60S acidic ribosomal protein P2 / Renal carcinoma antigen NY-REN-44


Mass: 7207.184 Da / Num. of mol.: 1 / Fragment: UNP residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPLP2, D11S2243E, RPP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P05387

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein_1-1, 1 mM [U-100% 13C; U-100% 15N] protein_2-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein_1-1[U-100% 13C; U-100% 15N]1
1 mMprotein_2-2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIABrunger, Adams, Clore, Gros, Nilges and Readchemical shift assignment
CNSrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 3

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