[English] 日本語
Yorodumi
- PDB-6y6m: solution structure of cold-shock domain 1 and 2 of drosophila Ups... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y6m
Titlesolution structure of cold-shock domain 1 and 2 of drosophila Upstream of N-Ras (Unr)
ComponentsUpstream of N-ras, isoform A
KeywordsRNA BINDING PROTEIN / CSD / ncCSD
Function / homology
Function and homology information


dosage compensation complex assembly / protein-RNA adaptor activity / RISC complex binding / sex differentiation / lncRNA binding / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cell differentiation / RNA binding / cytosol
Similarity search - Function
: / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins ...: / Cold shock domain-containing protein E1 CSD domain / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA-binding protein Unr
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsSimon, B. / Hollmann, N.M. / Hennig, J.
CitationJournal: Cell Rep / Year: 2020
Title: Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras.
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Masiewicz, P. / Guitart, T. / Simon, B. / Provaznik, J. / Stein, F. / Haberkant, P. / Sweetapple, L.J. / Villacorta, L. / Mooijman, D. / Benes, V. / ...Authors: Hollmann, N.M. / Jagtap, P.K.A. / Masiewicz, P. / Guitart, T. / Simon, B. / Provaznik, J. / Stein, F. / Haberkant, P. / Sweetapple, L.J. / Villacorta, L. / Mooijman, D. / Benes, V. / Savitski, M.M. / Gebauer, F. / Hennig, J.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 15, 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: Upstream of N-ras, isoform A


Theoretical massNumber of molelcules
Total (without water)18,4951
Polymers18,4951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11540 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Upstream of N-ras, isoform A


Mass: 18494.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GADDEE: residues from cleavage site/cloning overhang
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Unr, BcDNA:LD13080, CR32028, Dmel\CG7015, dUNR, MRE30, UNR, unr, CG7015, Dmel_CG7015
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VSK3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
122isotropic22D 1H-13C HSQC aliphatic
131isotropic13D CBCA(CO)NH
141isotropic13D HNCA
151isotropic13D HN(CA)CB
1121isotropic13D HN(CO)CA
1111isotropic12D 1H-15N HSQC
1102isotropic23D 1H-13C NOESY aliphatic
191isotropic23D HBHA(CO)NH
182isotropic23D (H)CCH-TOCSY
1132isotropic22D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution150 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 95% H2O/5% D2Oprotein in complex with RNA (AAA AAA AUG)dCSD12_H2O95% H2O/5% D2O
solution250 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 100% D2Oprotein in complex with RNA (AAA AAA AUG)dCSD12_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
10 mMDTTnatural abundance1
0.3 mMprotein[U-99% 13C; U-99% 15N]1
0.36 mMRNAnatural abundance1
50 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
10 mMDTTnatural abundance2
0.3 mMprotein[U-99% 13C; U-99% 15N]2
0.36 mMRNAnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

-
Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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