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- PDB-1iqt: Solution structure of the C-terminal RNA-binding domain of hetero... -

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Basic information

Entry
Database: PDB / ID: 1iqt
TitleSolution structure of the C-terminal RNA-binding domain of heterogeneous nuclear ribonucleoprotein D0 (AUF1)
Componentsheterogeneous nuclear ribonucleoprotein D0
KeywordsRNA BINDING PROTEIN / RNA-binding protein / hnRNP / AUF1 / telomere / DNA-binding protein
Function / homology
Function and homology information


hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / : / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / response to sodium phosphate / 3'-UTR-mediated mRNA destabilization ...hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / : / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / response to sodium phosphate / 3'-UTR-mediated mRNA destabilization / positive regulation of cytoplasmic translation / mRNA 3'-UTR AU-rich region binding / RNA catabolic process / regulation of telomere maintenance / telomeric DNA binding / positive regulation of telomere capping / minor groove of adenine-thymine-rich DNA binding / Processing of Capped Intron-Containing Pre-mRNA / cellular response to nitric oxide / response to electrical stimulus / RNA processing / mRNA Splicing - Major Pathway / cerebellum development / liver development / positive regulation of translation / cellular response to estradiol stimulus / AUF1 (hnRNP D0) binds and destabilizes mRNA / cellular response to amino acid stimulus / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / histone deacetylase binding / response to calcium ion / regulation of gene expression / postsynaptic density / ribonucleoprotein complex / negative regulation of gene expression / glutamatergic synapse / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
CARG-binding factor, N-terminal / CBFNT (NUC161) domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...CARG-binding factor, N-terminal / CBFNT (NUC161) domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein D0
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKatahira, M. / Miyanoiri, Y. / Enokizono, Y. / Matsuda, G. / Nagata, T. / Ishikawa, F. / Uesugi, S.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA.
Authors: Katahira, M. / Miyanoiri, Y. / Enokizono, Y. / Matsuda, G. / Nagata, T. / Ishikawa, F. / Uesugi, S.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Structure and Interactions with RNA of the N-Terminal UUAG-specific RNA-binding Domain of hnRNP D0
Authors: Nagata, T. / Kurihara, Y. / Matsuda, G. / Saeki, J. / Kohno, T. / Yanagida, Y. / Ishikawa, F. / Uesugi, S. / Katahira, M.
#2: Journal: Mol.Cell.Biol. / Year: 1993
Title: Nuclear Proteins That Bind the Pre-mRNA 3' Splice Site Sequence r(UUAG/G) and the Human Telomeric DNA Sequence d(TTAGGG)n
Authors: Ishikawa, F. / Matunis, M.J. / Dreyfuss, G. / Cech, T.R.
History
DepositionAug 1, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 27, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation_author ...atom_site / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation_author.name
Revision 2.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heterogeneous nuclear ribonucleoprotein D0


Theoretical massNumber of molelcules
Total (without water)8,6571
Polymers8,6571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5460 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
Representative

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Components

#1: Protein heterogeneous nuclear ribonucleoprotein D0 / AUF1


Mass: 8657.043 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14103

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1322D NOESY
1432D NOESY
153DQF-COSY
NMR detailsText: The structure was determined using 2D homonuclear and 3D 15N-edited heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM 15N labeled hnRNP D0 RBD2, 20mM sodium phosphate, 1mM sodium azide, 10mM deuterated DTT, small amounts of DSS95% H2O/5% D2O
22mM hnRNP D0 RBD2, 20mM sodium phosphate, 1mM sodium azide, 10mM deuterated DTT, small amounts of DSS95% H2O/5% D2O
32mM hnRNP D0 RBD2, 20mM sodium phosphate, 1mM sodium azide, 10mM deuterated DTT, small amounts of DSS100% D2O
Sample conditionsIonic strength: 0mM / pH: 6 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8Brungerstructure solution
CAPP/PIPP/STAPP4.2.5Garretdata analysis
XwinNMR2.6Brukerprocessing
X-PLOR3.8Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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