[English] 日本語
Yorodumi
- PDB-7prd: Solution structure of the chimeric Nrd1-Nab3 heterodimerization d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7prd
TitleSolution structure of the chimeric Nrd1-Nab3 heterodimerization domains
ComponentsProtein NRD1,HLJ1_G0022400.mRNA.1.CDS.1
KeywordsTRANSCRIPTION / Transcription termination / NNS pathway / Nab3 / Nrd1 / heterodimerization / chimera / yeast
Function / homology
Function and homology information


Nab3, RNA recognition motif / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / Anticodon-binding domain superfamily / RNA recognition motif / RNA recognition motif ...Nab3, RNA recognition motif / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / Anticodon-binding domain superfamily / 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
HLJ1_G0022400.mRNA.1.CDS.1 / Protein NRD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsChaves-Arquero, B. / Martinez-Lumbreras, S. / Perez-Canadillas, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Autonomous Community of MadridBMD-3770 Spain
CitationJournal: Life Sci Alliance / Year: 2022
Title: Structural basis of Nrd1-Nab3 heterodimerization.
Authors: Chaves-Arquero, B. / Martinez-Lumbreras, S. / Camero, S. / Santiveri, C.M. / Mirassou, Y. / Campos-Olivas, R. / Jimenez, M.A. / Calvo, O. / Perez-Canadillas, J.M.
History
DepositionSep 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein NRD1,HLJ1_G0022400.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)13,9441
Polymers13,9441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1medoid

-
Components

#1: Protein Protein NRD1,HLJ1_G0022400.mRNA.1.CDS.1


Mass: 13943.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCNYR20_0008007600, SCP684_0008007200, PACBIOSEQ_LOCUS5883
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6V8SAW3, UniProt: A0A6L0ZXA8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HNCO
151isotropic13D CBCA(CO)NH
161isotropic13D HN(CA)CB
172isotropic13D (H)CCH-TOCSY
184isotropic12D 1H-1H NOESY
195isotropic12D 1H-1H NOESY
1101isotropic13D 1H-15N NOESY
1113isotropic13D 1H-13C NOESY
1123isotropic13D 1H-13C HSQC NOESY 1H-13C HSQC

-
Sample preparation

Details
TypeSolution-IDLabelSolvent system
solution1CN_H2O90% H2O/10% D2O
solution2CN_D2O100% D2O
solution3methyl-lab100% D2O
solution4na_H2O90% H2O/10% D2O
solution5na_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium acetatenatural abundance1
25 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
1000 uMNrd1-Nab3 chimera[U-100% 13C; U-100% 15N]1
10 mMsodium acetatenatural abundance2
25 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
1000 uMNrd1-Nab3 chimera[U-100% 13C; U-100% 15N]2
10 mMsodium acetatenatural abundance3
25 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
1000 uMNrd1-Nab3 chimera13C - methyl (IVL)3
10 mMsodium acetatenatural abundance4
25 mMsodium chloridenatural abundance4
1 mMDTTnatural abundance4
1000 uMNrd1-Nab3 chimeranatural abundance4
10 mMsodium acetatenatural abundance5
25 mMsodium chloridenatural abundance5
1 mMDTTnatural abundance5
1000 uMNrd1-Nab3 chimeranatural abundance5
Sample conditionsIonic strength: 35 mM / Label: Conditions_1 / pH: 5.1 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
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