[English] 日本語
Yorodumi
- PDB-1rkj: Solution structure of the complex formed by the two N-terminal RN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rkj
TitleSolution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target
Components
  • 5'-R(*GP*GP*AP*UP*GP*CP*CP*UP*CP*CP*CP*GP*AP*GP*UP*GP*CP*AP*UP*CP*C)-3'
  • Nucleolin
KeywordsTranscription/RNA / Protein-RNA complex / RBD / Transcription-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of mRNA splicing, via spliceosome / telomeric DNA binding / spliceosomal complex / 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
RNA / RNA (> 10) / Nucleolin
Similarity search - Component
Biological speciesMesocricetus auratus (golden hamster)
MethodSOLUTION NMR / simulated annealing
AuthorsJohansson, C. / Finger, L.D. / Trantirek, L. / Mueller, T.D. / Kim, S. / Laird-Offringa, I.A. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target.
Authors: Johansson, C. / Finger, L.D. / Trantirek, L. / Mueller, T.D. / Kim, S. / Laird-Offringa, I.A. / Feigon, J.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999Authors think that the PRO 330 in the database sequence could be a sequencing error since the ...Authors think that the PRO 330 in the database sequence could be a sequencing error since the closely related mouse and rat sequences have leucines in this position. In addition, the codon usage for a leucine and a proline differs by only one nucleotide.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-R(*GP*GP*AP*UP*GP*CP*CP*UP*CP*CP*CP*GP*AP*GP*UP*GP*CP*AP*UP*CP*C)-3'
A: Nucleolin


Theoretical massNumber of molelcules
Total (without water)26,0462
Polymers26,0462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain 5'-R(*GP*GP*AP*UP*GP*CP*CP*UP*CP*CP*CP*GP*AP*GP*UP*GP*CP*AP*UP*CP*C)-3'


Mass: 6680.012 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE RNA IS NATURALLY FOUND IN the 5' ETS of Mus musculus (house mouse), EMBL accession M20154.
#2: Protein Nucleolin / Protein C23


Mass: 19365.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: NCL / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P08199

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 13C-separated NOESY
1243D 15N-separated NOESY
1332D 13C-filtered NOESY
2432D 13C-filtered NOESY
3532D 13C-filtered NOESY
164T1-coupled HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
1U-(15N,13C,99% 2H) nucleolin RBD12 in a 1 mM 1:1 complex with unlabeled b2NRE, 95% H2O, 5% D2O50 mM phosphate buffer, 95% H2O, 5% D2O
2U-(15N,13C,70% 2H) nucleolin RBD12 in a 1 mM 1:1 complex with unlabeled b2NRE, 95% H2O, 5% D2O50 mM phosphate buffer, 95% H2O, 5% D2O
3U-(15N,13C) nucleolin RBD12 in a 1 mM 1:1 complex with unlabeled b2NRE, 100% D2O50 mM phosphate buffer, 100% D2O
4U-(15N) nucleolin RBD12 in a 1 mM 1:1 complex with unlabeled b2NRE, 95% H2O, 5% D2O50 mM phosphate buffer, 95% H2O, 5% D2O
5Unlabeled nucleolin RBD12 in a 1mM 1:1 complex with 15N,13C-Adenine, Uracil labeled b2NRE, 100% D2O50 mM phosphate buffer, 100% D2O
6Unlabeled nucleolin RBD12 in a 1mM 1:1 complex with 15N,13C-Cytosine, Guanine labeled b2NRE, 100% D2O50 mM phosphate buffer, 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 mM KCl 7.0 ambient 310 K
250 mM KCl 7.0 ambient 310 K
3200 mM KCl 7.0 ambient 310 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX7503

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
Felix97BIOSYM Technologiesdata analysis
AURELIA3.108Brukerdata analysis
X-PLORNIHSchwieters, C.D., Kuszewski, J.J., Tjandra, N., Clore, G.M.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 3744 restraints, 3222 are NOE-derived distance constraints, 160 hydrogen bond restraints, 80 protein NH residual dipolar couplings, 250 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 14

+
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://pdbjlvh1.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