[English] 日本語
Yorodumi
- PDB-1x0f: Complex structure of the C-terminal RNA-binding domain of hnRNP D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x0f
TitleComplex structure of the C-terminal RNA-binding domain of hnRNP D(AUF1) with telomeric 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 / positive regulation of telomere capping ...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 telomere capping / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / RNA catabolic process / telomeric DNA binding / minor groove of adenine-thymine-rich DNA binding / Processing of Capped Intron-Containing Pre-mRNA / response to electrical stimulus / RNA processing / positive regulation of telomere maintenance via telomerase / cellular response to nitric oxide / mRNA Splicing - Major Pathway / positive regulation of translation / cerebellum development / AUF1 (hnRNP D0) binds and destabilizes mRNA / cellular response to amino acid stimulus / cellular response to estradiol stimulus / liver development / regulation of circadian rhythm / response to calcium ion / histone deacetylase binding / regulation of gene expression / postsynaptic density / ribonucleoprotein complex / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / glutamatergic synapse / 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.Biol.Chem. / Year: 2005
Title: Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by hnRNP D
Authors: Enokizono, Y. / Konishi, Y. / Nagata, K. / Ouhashi, K. / Uesugi, S. / Ishikawa, F. / Katahira, M.
#2: 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.
#3: 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.
#4: 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
DepositionMar 22, 2005Deposition 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 / 228structures with the lowest energy
RepresentativeModel #1lowest energy

-
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 / 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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1223D 15N-separated TOCSY
1344D 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 2D homonuclear and 3D heteronuclear techniques.

-
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

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERstructure solution
NMRPipeprocessing
XwinNMRprocessing
X-PLOR3.851BRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 228 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more