[English] 日本語
Yorodumi
- PDB-1fjc: SOLUTION STRUCTURE OF NUCLEOLIN RBD2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fjc
TitleSOLUTION STRUCTURE OF NUCLEOLIN RBD2
ComponentsNUCLEOLIN RBD2
KeywordsSTRUCTURAL PROTEIN / RNP / RBD / RRM / RNA binding domain / Nucleolus
Function / homology
Function and homology information


telomeric DNA binding / ribonucleoprotein complex / nucleolus / RNA binding / cytoplasm
Similarity search - Function
Nucleolin, RNA recognition motif 1 / Nucleolin, RNA recognition motif 2 / Nucleolin, RNA recognition motif 3 / Nucleolin, RNA recognition motif 4 / 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 ...Nucleolin, RNA recognition motif 1 / Nucleolin, RNA recognition motif 2 / Nucleolin, RNA recognition motif 3 / Nucleolin, RNA recognition motif 4 / 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
Biological speciesMesocricetus auratus (golden hamster)
MethodSOLUTION NMR / simulated annealing using XPLOR 3.841
AuthorsAllain, F.H.-T. / Gilbert, D.E. / Bouvet, P. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Solution structure of the two N-terminal RNA-binding domains of nucleolin and NMR study of the interaction with its RNA target.
Authors: Allain, F.H. / Gilbert, D.E. / Bouvet, P. / Feigon, J.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NUCLEOLIN RBD2


Theoretical massNumber of molelcules
Total (without water)10,6721
Polymers10,6721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)33 / 50all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein NUCLEOLIN RBD2 / PROTEIN C23


Mass: 10671.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P08199

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
2322D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N,13C; 50mM potassium phosphate buffer; 100 mM KCl, 5mM deuterated DTT, pH 6.290% H2O/10% D2O
21mM U-15N,13C; 50mM potassium phosphate buffer; 100 mM KCl, 5mM deuterated DTT, pH 6.2100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 6.2 ambient 293 K
2150 6.2 ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.841Brungerrefinement
X-PLOR3.841Brungerstructure solution
DYANA1Guntertstructure solution
RefinementMethod: simulated annealing using XPLOR 3.841 / Software ordinal: 1
Details: structures are based on 1279 restraints, 1209 are NOE-derived and 70 are from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 33

+
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