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- PDB-7vb2: Solution structure of human ribosomal protein uL11 -

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Basic information

Entry
Database: PDB / ID: 7vb2
TitleSolution structure of human ribosomal protein uL11
Components60S ribosomal protein L12
KeywordsRIBOSOMAL PROTEIN / translation / elongation factors
Function / homology
Function and homology information


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 ...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) / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / postsynaptic density / structural constituent of ribosome / translation / focal adhesion / nucleolus / RNA binding / extracellular exosome / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12
Similarity search - Domain/homology
Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsLee, K.M. / Wong, K.B.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The flexible N-terminal motif of uL11 unique to eukaryotic ribosomes interacts with P-complex and facilitates protein translation.
Authors: Yang, L. / Lee, K.M. / Yu, C.W. / Imai, H. / Choi, A.K. / Banfield, D.K. / Ito, K. / Uchiumi, T. / Wong, K.B.
History
DepositionAug 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 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

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Assembly

Deposited unit
A: 60S ribosomal protein L12


Theoretical massNumber of molelcules
Total (without water)17,8481
Polymers17,8481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13810 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 900structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein 60S ribosomal protein L12 / Large ribosomal subunit protein uL11


Mass: 17847.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL12 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P30050

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D HN(CA)CB
122isotropic13D CBCA(CO)NH
132isotropic13D HNCA
142isotropic13D HN(CO)CA
152isotropic13D HNCO
162isotropic13D HN(CA)CO
171isotropic12D 1H-15N HSQC
182isotropic12D 1H-13C HSQC
191isotropic13D 1H-15N TOCSY
1102isotropic13D (H)CCH-TOCSY
1112isotropic13D (H)CCH-COSY
1122isotropic13D HBHA(CO)NH
1132isotropic13D (H)CC(CO)NH
1142isotropic13D H(CC)(CO)NH
1153isotropic12D 1H-1H NOESY
1163isotropic12D 1H-1H TOCSY
1171isotropic13D 1H-15N NOESY
1182isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3 mM [U-15N] human uL11, 20 mM sodium phosphate, 50 mM sodium sulfate, 0.3 % w/v CHAPS, 5 mM DTT, 95% H2O/5% D2O15N_uL1195% H2O/5% D2O
solution20.3 mM [U-13C; U-15N] human uL11, 20 mM sodium phosphate, 50 mM sodium sulfate, 0.3 % w/v CHAPS, 5 mM DTT, 95% H2O/5% D2O13C15N_uL1195% H2O/5% D2O
solution30.3 mM human uL11, 20 mM sodium phosphate, 50 mM sodium sulfate, 0.3 % w/v CHAPS, 5 mM DTT, 95% H2O/5% D2Ounlabel_uL1195% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMhuman uL11[U-15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium sulfatenatural abundance1
0.3 % w/vCHAPSnatural abundance1
5 mMDTTnatural abundance1
0.3 mMhuman uL11[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium sulfatenatural abundance2
0.3 % w/vCHAPSnatural abundance2
5 mMDTTnatural abundance2
0.3 mMhuman uL11natural abundance3
20 mMsodium phosphatenatural abundance3
50 mMsodium sulfatenatural abundance3
0.3 % w/vCHAPSnatural abundance3
5 mMDTTnatural abundance3
Sample conditionsIonic strength: 20mM sodium phosphate,50mM sodium sulfate mM
Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 306 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
NMRViewJOne Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 900 / Conformers submitted total number: 10

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