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- PDB-1wh9: Solution structure of the KH domain of human ribosomal protein S3 -

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Basic information

Entry
Database: PDB / ID: 1wh9
TitleSolution structure of the KH domain of human ribosomal protein S3
Components40S ribosomal protein S3
KeywordsRIBOSOME / KH domain / Structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of endodeoxyribonuclease activity / negative regulation of DNA repair / oxidized purine DNA binding / supercoiled DNA binding / NF-kappaB complex ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of endodeoxyribonuclease activity / negative regulation of DNA repair / oxidized purine DNA binding / supercoiled DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / Formation of the ternary complex, and subsequently, the 43S complex / protein kinase A binding / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / SARS-CoV-1 modulates host translation machinery / 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 / spindle assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / positive regulation of JUN kinase activity / positive regulation of microtubule polymerization / negative regulation of protein ubiquitination / DNA-(apurinic or apyrimidinic site) endonuclease activity / Hsp70 protein binding / translational initiation / positive regulation of DNA repair / positive regulation of interleukin-2 production / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / tubulin binding / DNA endonuclease activity / chromosome segregation / positive regulation of apoptotic signaling pathway / Hsp90 protein binding / positive regulation of protein-containing complex assembly / base-excision repair / mitotic spindle / kinase binding / Regulation of expression of SLITs and ROBOs / ruffle membrane / cellular response to hydrogen peroxide / cellular response to reactive oxygen species / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / small ribosomal subunit rRNA binding / SARS-CoV-2 modulates host translation machinery / microtubule binding / regulation of apoptotic process / cytosolic small ribosomal subunit / DNA-binding transcription factor binding / mitochondrial inner membrane / damaged DNA binding / cytoplasmic translation / postsynaptic density / negative regulation of translation / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / cell division / DNA repair / focal adhesion / mRNA binding / apoptotic process / DNA damage response / positive regulation of gene expression / protein-containing complex binding / nucleolus / protein kinase binding / enzyme binding / endoplasmic reticulum / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain ...K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsNameki, N. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the KH domain of human ribosomal protein S3
Authors: Nameki, N. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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: 40S ribosomal protein S3


Theoretical massNumber of molelcules
Total (without water)9,9171
Polymers9,9171
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)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein 40S ribosomal protein S3 / ribosomal protein S3


Mass: 9917.071 Da / Num. of mol.: 1 / Fragment: KH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: IMS cDNA adKA01519 / Plasmid: P040301-10 / References: UniProt: P23396

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.6mM KH domain U-15N, 13C; d-Tris-HCl(pH 7.0); 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 220mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.901Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
OPALpKoradi, R.,Billeter, M.,Guentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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