[English] 日本語
Yorodumi
- PDB-2kjm: Solution structure of SLBP RNA binding domain fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kjm
TitleSolution structure of SLBP RNA binding domain fragment
ComponentsHistone RNA hairpin-binding protein
KeywordsRNA BINDING PROTEIN / SLBP / histone mRNA / Stem-Loop Binding Protein / Hairpin Binding Protein / mRNA processing / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / histone pre-mRNA DCP binding / histone pre-mRNA 3'end processing complex / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of the SLBP Dependant Mature mRNA / RNA Polymerase II Transcription Termination / mRNA transport ...histone mRNA stem-loop binding complex / histone pre-mRNA stem-loop binding / mRNA 3'-end processing by stem-loop binding and cleavage / cap-dependent translational initiation / histone pre-mRNA DCP binding / histone pre-mRNA 3'end processing complex / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of the SLBP Dependant Mature mRNA / RNA Polymerase II Transcription Termination / mRNA transport / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Histone RNA stem-loop-binding protein SLBP1/SLBP2 / Histone RNA hairpin-binding protein, RNA-binding domain / SLBP, RNA-binding domain superfamily / Histone RNA hairpin-binding protein RNA-binding domain
Similarity search - Domain/homology
Histone RNA hairpin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsThapar, R.
CitationJournal: Biochemistry / Year: 2012
Title: Interaction of the histone mRNA hairpin with stem-loop binding protein (SLBP) and regulation of the SLBP-RNA complex by phosphorylation and proline isomerization.
Authors: Zhang, M. / Lam, T.T. / Tonelli, M. / Marzluff, W.F. / Thapar, R.
History
DepositionJun 3, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone RNA hairpin-binding protein


Theoretical massNumber of molelcules
Total (without water)3,6681
Polymers3,6681
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)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Histone RNA hairpin-binding protein / Histone stem-loop-binding protein


Mass: 3668.141 Da / Num. of mol.: 1 / Fragment: UNP residues 129-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLBP, HBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q14493

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the N-terminal 30 residue peptide from the RNA binding and processing domain of Stem-Loop Binding Protein (SLBP) that binds a 26 nucleotide hairpin in the 3' untranslated region of histone mRNAs.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

-
Sample preparation

DetailsContents: 1-7 mM SLBP30mer-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: SLBP30mer-1 / Conc. range: 1-7
Sample conditionsIonic strength: 0.050 / pH: 5 / Pressure: ambient / Temperature: 278 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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://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