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- PDB-4beh: Solution structure of human ribosomal protein P1.P2 heterodimer -

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Basic information

Entry
Database: PDB / ID: 4beh
TitleSolution structure of human ribosomal protein P1.P2 heterodimer
Components
  • 60S ACIDIC RIBOSOMAL PROTEIN P1
  • 60S ACIDIC RIBOSOMAL PROTEIN P2
KeywordsTRANSLATION / STALK / RIBOSOME
Function / homology
Function and homology information


PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / negative regulation of myoblast fusion / cytoplasmic translational elongation / translational elongation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / protein kinase activator activity ...PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / negative regulation of myoblast fusion / cytoplasmic translational elongation / translational elongation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / protein kinase activator activity / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ribonucleoprotein complex binding / 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 / striated muscle contraction / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / spermatogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / focal adhesion / endoplasmic reticulum / 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 P1 / Large ribosomal subunit protein P2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA
AuthorsLee, K.M. / Yusa, K. / Chu, L.O. / Wing-Heng Yu, C. / Shaw, P.C. / Oono, M. / Miyoshi, T. / Ito, K. / Wong, K.B. / Uchiumi, T.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Solution Structure of Human P1P2 Heterodimer Provides Insights Into the Role of Eukaryotic Stalk in Recruiting the Ribosome-Inactivating Protein Trichosanthin to the Ribosome.
Authors: Lee, K.M. / Yusa, K. / Chu, L.O. / Wing-Heng Yu, C. / Oono, M. / Miyoshi, T. / Ito, K. / Shaw, P.C. / Wong, K.B. / Uchiumi, T.
History
DepositionMar 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 2.0Jun 14, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_validate_close_contact
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)23,2702
Polymers23,2702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
RepresentativeModel #8

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Components

#1: Protein 60S ACIDIC RIBOSOMAL PROTEIN P1


Mass: 11521.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P05386
#2: Protein 60S ACIDIC RIBOSOMAL PROTEIN P2 / RENAL CARCINOMA ANTIGEN NY-REN-44


Mass: 11747.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P05387

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ASYMMETRICALLY LABELED P1.P2 HETERODIMER. C13,N15P1.P2 AND P1.C13,N15P2.

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,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 AND LOWEST ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 20

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