[English] 日本語
Yorodumi
- PDB-7pre: Solution structure of the NRDI domain of Nab3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pre
TitleSolution structure of the NRDI domain of Nab3
ComponentsHLJ1_G0022400.mRNA.1.CDS.1
KeywordsTRANSCRIPTION / Transcription termination / NNS pathway / yeast / Nab3 / heterodimerization domain
Function / homology
Function and homology information


Nab3, RNA recognition motif / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLJ1_G0022400.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)6,1071
Polymers6,1071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5210 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1medoid

-
Components

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


Mass: 6106.913 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS5883 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L0ZXA8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
124isotropic12D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HNCO
151isotropic13D CBCA(CO)NH
161isotropic13D HN(CA)CB
174isotropic13D (H)CCH-TOCSY
192isotropic12D 1H-1H NOESY
183isotropic12D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution125 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 480 uM [U-100% 13C; U-100% 15N] Nab3, 90% H2O/10% D2OH2O-CN90% H2O/10% D2O
solution225 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 480 uM Nab3, 90% H2O/10% D2OH2O-na90% H2O/10% D2O
solution325 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 480 uM Nab3, 100% D2OD2O-na100% D2O
solution425 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 480 uM [U-100% 13C; U-100% 15N] Nab3, 100% D2OD2O-CN100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMpotassium phosphatenatural abundance1
25 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
480 uMNab3[U-100% 13C; U-100% 15N]1
25 mMpotassium phosphatenatural abundance2
25 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
480 uMNab3natural abundance2
25 mMpotassium phosphatenatural abundance3
25 mMsodium chloridenatural abundance3
1 mMDTTnatural abundance3
480 uMNab3natural abundance3
25 mMpotassium phosphatenatural abundance4
25 mMsodium chloridenatural abundance4
1 mMDTTnatural abundance4
480 uMNab3[U-100% 13C; U-100% 15N]4
Sample conditionsIonic strength: 53.5 mM / Label: conditions1 / pH: 6.6 / Pressure: 1 atm / Temperature: 308 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