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- PDB-1ck2: YEAST (SACCHAROMYCES CEREVISIAE) RIBOSOMAL PROTEIN L30 -

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Basic information

Entry
Database: PDB / ID: 1ck2
TitleYEAST (SACCHAROMYCES CEREVISIAE) RIBOSOMAL PROTEIN L30
Components60S RIBOSOMAL PROTEIN L30
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / AUTO-REGULATION OF PRE-MRNA SPLICING AND MRNA TRANSLATION
Function / homology
Function and homology information


pre-mRNA 5'-splice site binding / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / rRNA processing / cytosolic large ribosomal subunit ...pre-mRNA 5'-splice site binding / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / rRNA processing / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / RNA binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMIC
AuthorsMao, H. / Willamson, J.R.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Local folding coupled to RNA binding in the yeast ribosomal protein L30
Authors: Mao, H. / Williamson, J.R.
#1: Journal: J.Biol.Chem. / Year: 1987
Title: The Yeast Ribosomal Protein L32 and its Gene
Authors: Dabeva, M.D. / Warner, J.R.
History
DepositionApr 26, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: 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 RIBOSOMAL PROTEIN L30


Theoretical massNumber of molelcules
Total (without water)11,2991
Polymers11,2991
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)1 / 50LOWEST TOTAL ENERGY
Representative

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Components

#1: Protein 60S RIBOSOMAL PROTEIN L30 / RL30_YEAST


Mass: 11299.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This entry, 1CK2, is the replacement of 1CN6 cited in the primary reference
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: RECOMBINANT EXPRESSION AS A C-TERMINAL MALTOSE-BINDING PROTEIN FUSION IN ESCHERICHIA COLI STRAIN JM109 HOSTING PLASMID PMALC-30
Cellular location: CYTOPLASM / Gene: RPL30 / Organelle: RIBOSOME, 60S SUBUNIT / Plasmid: PMALC-L30 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14120

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HNCA
151HNCO
161HN(CO)CA
171CBCA(CO)NH
181HCCHTOCSY
191NOESYHSQC
NMR detailsText: MEAN STRUCTURE. THIS STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED L30 PROTEIN.

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 300 mM / pH: 6.5 / Pressure: 1 ATOM / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian VARIAN INOVA / Manufacturer: Varian / Model: VARIAN INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
NMRDrawstructure solution
NMRPipestructure solution
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMIC / Software ordinal: 1
Details: DISTANCE INTRARESIDUE NOES 720 INTERRESIDUE NOES 698 SEQUENTIAL (|I-J|=1) 291 SHORT-RANGE (|I-J|<=4) 149, LONG-RANGE (|I-J|>4) 258, HYDROGEN BONDS 62. TOTAL 1418, TORSION BACKBONE PHI 80, SIDECHAIN KAI1 59, TOTAL 139
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 1

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