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- PDB-1wtb: Complex structure of the C-terminal RNA-binding domain of hnRNP D... -

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Basic information

Entry
Database: PDB / ID: 1wtb
TitleComplex structure of the C-terminal RNA-binding domain of hnRNP D (AUF1) with telomere DNA
Components
  • 5'-D(P*TP*AP*GP*G)-3'
  • Heterogeneous nuclear ribonucleoprotein D0
KeywordsTRANSCRIPTION/DNA / RNA-binding domain / DNA-binding domain / RRM / hnRNP D / AUF1 / Telomere / Complex / structural genomics / TRANSCRIPTION-DNA COMPLEX
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 / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / 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 / RNA processing / response to electrical stimulus / mRNA Splicing - Major Pathway / cerebellum development / liver development / cellular response to estradiol stimulus / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of translation / 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
DNA / Heterogeneous nuclear ribonucleoprotein D0
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsEnokizono, Y. / Konishi, Y. / Nagata, K. / Ouhashi, K. / Uesugi, S. / Ishikawa, F. / Katahira, M.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D
Authors: Enokizono, Y. / Konishi, Y. / Nagata, K. / Ouhashi, K. / Uesugi, S. / Ishikawa, F. / Katahira, M.
#1: 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.
#2: 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.
#3: 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
DepositionNov 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(P*TP*AP*GP*G)-3'
A: Heterogeneous nuclear ribonucleoprotein D0


Theoretical massNumber of molelcules
Total (without water)10,3342
Polymers10,3342
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(P*TP*AP*GP*G)-3'


Mass: 1230.854 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Heterogeneous nuclear ribonucleoprotein D0 / AUF1 / hnRNP D0 / AU-rich element RNA-binding protein 1


Mass: 9103.628 Da / Num. of mol.: 1 / Fragment: C-terminal RNA-binding 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
1123D 15N-separated NOESY
1223D 15N-separated TOCSY
1343D 13C-separated NOESY
1423D HNHA
1513D HNCA
164(H)CCH-TOCSY
174(H)CCH-COSY
1821H, 15N-HSQC
1952D ROESY
11052D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM U-13C, 15N hnRNP D BD2, 2.4mM DNA, 20mM Sodium Phosphate, 10mM Deuterated DTT, 1mM Sodium Azide95% H2O/5% D2O
22mM U-15N hnRNP D BD2, 2.4mM DNA, 20mM Sodium Phosphate, 10mM Deuterated DTT, 1mM Sodium Azide95% H2O/5% D2O
32mM hnRNP D BD2, 2.4mM DNA, 20mM Sodium Phosphate, 10mM Deuterated DTT, 1mM Sodium Azide95% H2O/5% D2O
42mM U-13C, 15N hnRNP D BD2, 2.4mM DNA, 20mM Sodium Phosphate, 10mM Deuterated DTT, 1mM Sodium Azide100% D2O
52mM U-15N hnRNP D BD2, 2.4mM DNA, 20mM Sodium Phosphate, 10mM Deuterated DTT, 1mM Sodium Azide100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERstructure solution
NMRPipeprocessing
XwinNMRcollection
X-PLOR3.851refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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