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- PDB-2dkl: Solution Structure of the UBA Domain in the Human Trinucleotide R... -

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Basic information

Entry
Database: PDB / ID: 2dkl
TitleSolution Structure of the UBA Domain in the Human Trinucleotide Repeat Containing 6C Protein (hTNRC6C)
ComponentsTrinucleotide Repeat Containing 6C Protein
KeywordsSIGNALING PROTEIN / Trinucleotide Repeat Containing 6C Protein / TNRC6C / KIAA1582 protein / UBA domain / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / Transcriptional Regulation by MECP2 / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / Regulation of MITF-M-dependent genes involved in apoptosis / TGFBR3 expression ...Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / Transcriptional Regulation by MECP2 / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / Regulation of MITF-M-dependent genes involved in apoptosis / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / TP53 Regulates Metabolic Genes / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAPK6/MAPK4 signaling / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA binding / nucleoplasm / cytosol
Similarity search - Function
TNRC6C, RNA recognition motif / Trinucleotide repeat-containing gene 6C protein, UBA domain / GW182, middle domain / M domain of GW182 / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / : / Argonaute hook / UBA/TS-N domain ...TNRC6C, RNA recognition motif / Trinucleotide repeat-containing gene 6C protein, UBA domain / GW182, middle domain / M domain of GW182 / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / : / Argonaute hook / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / RNA recognition motif / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Trinucleotide repeat-containing gene 6C protein / Trinucleotide repeat-containing gene 6C protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsZhao, C. / Kigawa, T. / Yoneyama, M. / Koshiba, S. / Harada, T. / Watanabe, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the UBA Domain in the Human Trinucleotide Repeat Containing 6C Protein (hTNRC6C)
Authors: Zhao, C. / Kigawa, T. / Yoneyama, M. / Koshiba, S. / Harada, T. / Watanabe, S. / Yokoyama, S.
History
DepositionApr 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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:
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Assembly

Deposited unit
A: Trinucleotide Repeat Containing 6C Protein


Theoretical massNumber of molelcules
Total (without water)8,9521
Polymers8,9521
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Trinucleotide Repeat Containing 6C Protein / KIAA1582 protein / TNRC6C


Mass: 8952.071 Da / Num. of mol.: 1 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KIAA1582 / Plasmid: P051216-11 / Production host: Cell free synthesis / References: UniProt: Q86UE5, UniProt: Q9HCJ0*PLUS

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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: 1.13mM UBA domain U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9732Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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