[English] 日本語
Yorodumi
- PDB-2dhs: Solution Structure of Nucleic Acid Binding Protein CUGBP1ab and i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dhs
TitleSolution Structure of Nucleic Acid Binding Protein CUGBP1ab and its Binding Study with DNA and RNA
ComponentsCUG triplet repeat RNA-binding protein 1
KeywordsRNA BINDING PROTEIN / beta sheet / two helices packed against the beta sheet
Function / homology
Function and homology information


BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / mRNA destabilization / regulation of alternative mRNA splicing, via spliceosome / germ cell development ...BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / mRNA destabilization / regulation of alternative mRNA splicing, via spliceosome / germ cell development / regulation of RNA splicing / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / mRNA processing / cytoplasmic stress granule / regulation of inflammatory response / ribonucleoprotein complex / negative regulation of cell population proliferation / negative regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / 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 ...CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / 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
CUGBP Elav-like family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsXia, Y.L. / Jun, K.Y. / Zhu, Q. / Han, X.G. / Zhang, H. / Timchenko, L. / Swanson, M. / Gao, X.L.
CitationJournal: To be Published
Title: Solution Structure of Nucleic Acid Binding Protein CUGBP1ab and its Binding Study with DNA and RNA
Authors: Xia, Y.L. / Jun, K.Y. / Zhu, Q. / Han, X.G. / Zhang, H. / Timchenko, L. / Swanson, M. / Gao, X.L.
History
DepositionMar 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CUG triplet repeat RNA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)21,1061
Polymers21,1061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein CUG triplet repeat RNA-binding protein 1 / CUG-BP1 / RNA-binding protein BRUNOL-2 / Deadenylation factor CUG-BP / 50 kDa Nuclear ...CUG-BP1 / RNA-binding protein BRUNOL-2 / Deadenylation factor CUG-BP / 50 kDa Nuclear polyadenylated RNA-binding protein / EDEN-BP


Mass: 21106.293 Da / Num. of mol.: 1 / Fragment: RRM1 and RRM2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUGBP1 (AMINO ACIDS 1 - 187) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q92879

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D HSQC
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HBHANH
1913D HBHA(CO)NH
11013D 15N-separated NOESY
11113D 13C-separated NOESY
11214D 13C-separated NOESY
11314D 13C/15N-separated NOESY
1141HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. The both two domains RRM1 (RNA recognition motif) and RRM2 contain the same beta-alpha-beta-beta-alpha-beta topology as ...Text: The structure was determined using triple-resonance NMR spectroscopy. The both two domains RRM1 (RNA recognition motif) and RRM2 contain the same beta-alpha-beta-beta-alpha-beta topology as expected for RNA-recognition motif. The four beta strands form an anti parallel beta sheet. The two alpha helices are packed against the beta sheet. Other NMR experiments including 15N T1 and T2 and {1H}-15N steady state NOE, and titration with DNA and RNA, were carried out. the RRM1 shows more conformat on exchange than RRM2. The N-terminal region and the linker between the RRM1 and RRM2 show more flexibility than other regions. In addition, two loops L3 and L5 in RRM1 also demonstrate considerable flexibility and conformation exchange. The conformation exchange and flexibility in the RRM1 may be utilized in the recognition process by allowing different conformational states to be accessed and facilitating induced fit for complex forming. From the titration experiments,we found that the (GTC)3 and (GUCU)3 mainly bind the two central beta strands of the RRM1 and the linker of the RRM1 and RRM2 domains.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O90% H2O/10% D2O
20.6mM CUGBP1ab U-15N; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 100% D2O100% D2O
Sample conditionsIonic strength: 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA
pH: 5.8 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Frank Delaglio Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Baxprocessing
Sparky3.112T. D. Goddard and D. G. Knellerdata analysis
ARIA2.0alphaMichael Habeck, Wolfgang Rieping,Jens Linge and Michael Nilgesstructure solution
ARIA2.0alphaMichael Habeck, Wolfgang Rieping,Jens Linge and Michael Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The protein CUGBP1ab has total 187 residues (residues 1-187 of CUGBP1) including an N-terminus Histag-thrombin site (21 amino acids) and 20 amino acids in the C-terminus which is from the ...Details: The protein CUGBP1ab has total 187 residues (residues 1-187 of CUGBP1) including an N-terminus Histag-thrombin site (21 amino acids) and 20 amino acids in the C-terminus which is from the plasmid. The molecular weight of the CUGBP1ab is 25.4 kDa. The structures are based on a total of 4228 restraints, 3776 are NOE-derived distance donstraints, 324 dihedral angle restraints,128 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 7

+
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