[English] 日本語
Yorodumi
- PDB-5o1t: Solution structure of the RNA binding domain of Nrd1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o1t
TitleSolution structure of the RNA binding domain of Nrd1
ComponentsProtein NRD1
KeywordsRNA BINDING PROTEIN / Nrd1 / RRM / RNA-binding / transcription non-coding RNAs
Function / homology
Function and homology information


transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / CUT catabolic process / snRNA 3'-end processing / tRNA 3'-end processing / nuclear mRNA surveillance / mRNA 3'-end processing ...transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / CUT catabolic process / snRNA 3'-end processing / tRNA 3'-end processing / nuclear mRNA surveillance / mRNA 3'-end processing / protein domain specific binding / mRNA binding / RNA binding / nucleus
Similarity search - Function
: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / 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
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Minimization
AuthorsMartinez-Lumbreras, S. / Perez-Canadillas, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spain
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition.
Authors: Franco-Echevarria, E. / Gonzalez-Polo, N. / Zorrilla, S. / Martinez-Lumbreras, S. / Santiveri, C.M. / Campos-Olivas, R. / Sanchez, M. / Calvo, O. / Gonzalez, B. / Perez-Canadillas, J.M.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein NRD1


Theoretical massNumber of molelcules
Total (without water)20,0521
Polymers20,0521
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 area10010 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1medoid

-
Components

#1: Protein Protein NRD1


Mass: 20051.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NRD1, YNL251C, N0868 / Production host: Escherichia coli (E. coli) / References: UniProt: P53617

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic23D HNCA
141isotropic23D HNCO
151isotropic23D CBCA(CO)NH
161isotropic23D (H)CCH-TOCSY
172isotropic22D 1H-1H NOESY
1131isotropic23D 1H-15N NOESY
1143isotropic22D 1H-1H NOESY F1filtered
1154isotropic22D 1H-1H NOESY F1filtered
1165isotropic22D 1H-1H NOESY F1filtered

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1600 uM [U-100% 13C; U-100% 15N] Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_CN90% H2O/10% D2O
solution2800 uM Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_na90% H2O/10% D2O
solution3400 uM [U-100% 13C; U-100% 15N] expect for Phe and Leu residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_PheLeu90% H2O/10% D2O13C 15N sample uniformly unlabelled in Phe and Leu (12C/14N)
solution4400 uM [U-100% 13C; U-100% 15N] expect for Ile residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_Ile90% H2O/10% D2O13C 15N sample uniformly unlabelled in Ile (12C/14N)
solution5400 uM [U-100% 13C; U-100% 15N] expect for Arg residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2ONrd1_Arg90% H2O/10% D2O13C 15N sample uniformly unlabelled in Arg (12C/14N)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMNrd1[U-100% 13C; U-100% 15N]1
25 mMpotassium phosphatenatural abundance1
25 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
800 uMNrd1natural abundance2
25 mMpotassium phosphatenatural abundance2
25 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
400 uMNrd1[U-100% 13C; U-100% 15N] expect for Phe and Leu residues3
25 mMpotassium phosphatenatural abundance3
25 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
400 uMNrd1[U-100% 13C; U-100% 15N] expect for Ile residues4
25 mMpotassium phosphatenatural abundance4
25 mMsodium chloridenatural abundance4
1 mMDTTnatural abundance4
400 uMNrd1[U-100% 13C; U-100% 15N] expect for Arg residues5
25 mMpotassium phosphatenatural abundance5
25 mMsodium chloridenatural abundance5
1 mMDTTnatural abundance5
Sample conditionsIonic strength: 59.1 mM / Label: Nrd1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: Minimization / Software ordinal: 5
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / 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