[English] 日本語
Yorodumi
- PDB-1rgo: Structural Basis for Recognition of the mRNA Class II AU-Rich Ele... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rgo
TitleStructural Basis for Recognition of the mRNA Class II AU-Rich Element by the Tandem Zinc Finger Domain of TIS11d
Components
  • Butyrate response factor 2
  • RNA (5'-R(*UP*UP*AP*UP*UP*UP*AP*UP*U)-3')
KeywordsRNA BINDING PROTEIN / TIS11 TTP tristetraprolin butyrate response factor ERF Nup475 ZFP Zn zinc finger RNA ss single-stranded ARE UTR tandem intercalation intercalate specific
Function / homology
Function and homology information


negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / negative regulation of stem cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / M-decay: degradation of maternal mRNAs by maternally stored factors / definitive hemopoiesis / cellular response to fibroblast growth factor stimulus ...negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / negative regulation of stem cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / M-decay: degradation of maternal mRNAs by maternally stored factors / definitive hemopoiesis / cellular response to fibroblast growth factor stimulus / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / cellular response to glucocorticoid stimulus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / negative regulation of fat cell differentiation / somatic stem cell population maintenance / mRNA catabolic process / hemopoiesis / cellular response to epidermal growth factor stimulus / cellular response to transforming growth factor beta stimulus / regulation of mRNA stability / ERK1 and ERK2 cascade / response to wounding / cellular response to tumor necrosis factor / T cell differentiation in thymus / ribonucleoprotein complex / RNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Tis11B-like protein, N-terminal / RNA-binding protein ZFP36-like / Tis11B like protein, N terminus / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
RNA / mRNA decay activator protein ZFP36L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Individual zinc finger domains were created in DYANA, docked to UAUU (finger I), UUAUU (finger II) using five rounds of simulated annealing in AMBER using distance, torsional restraints. Finger I, UAUU, Finger II, UUAUU complexes were connected to form TZF, UUAUUUAUU complexes, refined in AMBER with residual dipolar coupling restraints added. Calculations were then switched from in vacuo to Generalized Born continuum solvent model, one additional round of simulated annealing was performed.
AuthorsHudson, B.P. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
CitationJournal: NAT.STRUCT.MOL.BIOL. / Year: 2004
Title: Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d.
Authors: Hudson, B.P. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionNov 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: RNA (5'-R(*UP*UP*AP*UP*UP*UP*AP*UP*U)-3')
A: Butyrate response factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2034
Polymers11,0722
Non-polymers1312
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

-
Components

#1: RNA chain RNA (5'-R(*UP*UP*AP*UP*UP*UP*AP*UP*U)-3')


Mass: 2756.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic
#2: Protein Butyrate response factor 2 / TIS11D protein / EGF-response factor 2 / ERF-2


Mass: 8315.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZFP36L2, BRF2, TIS11D, ERF2 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P47974
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1233D 13C-separated NOESY
1333D 13C F1-edited, F3-filtered NOESY
1432D 13C double-half-filtered NOESY
151HNHA
161HNHB
173HACAHB COSY
18313C-{13CO} spin-echo difference CT-HSQC
19313C-{15N} spin-echo difference CT-HSQC
1104IPAP-[1H-15N]-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM 15N-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO495% H2O, 5% D20
20.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO495% H2O/5% D2O
30.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4100% D2O
40.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO4; 12 mg/mL Pf1 bacteriophage95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM KCl / pH: 6.2 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker DMXBrukerDMX7502
Bruker AVANCEBrukerAVANCE9003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMRvariousBrukercollection
NMRPipeDelaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer J.; Bax, A.processing
NMRView5Johnson, B. A. & Blevins, R. A.data analysis
SANEDuggan, B. M.data analysis
DYANA1.5Guntert, P.; Mumenthaler, C.; Wuthrich, K.structure solution
Amber8Case, D. A., et al.structure solution
Amber8Case, D. A., et al.refinement
RefinementMethod: Individual zinc finger domains were created in DYANA, docked to UAUU (finger I), UUAUU (finger II) using five rounds of simulated annealing in AMBER using distance, torsional restraints. ...Method: Individual zinc finger domains were created in DYANA, docked to UAUU (finger I), UUAUU (finger II) using five rounds of simulated annealing in AMBER using distance, torsional restraints. Finger I, UAUU, Finger II, UUAUU complexes were connected to form TZF, UUAUUUAUU complexes, refined in AMBER with residual dipolar coupling restraints added. Calculations were then switched from in vacuo to Generalized Born continuum solvent model, one additional round of simulated annealing was performed.
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

+
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://pdbjlvh1.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