[English] 日本語
Yorodumi
- PDB-4b8t: RNA BINDING PROTEIN Solution structure of the third KH domain of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b8t
TitleRNA BINDING PROTEIN Solution structure of the third KH domain of KSRP in complex with the G-rich target sequence.
Components
  • 5'-R(*AP*GP*GP*GP*UP)-3'
  • KH-TYPE SPLICING REGULATORY PROTEIN
KeywordsTRANSCRIPTION/RNA / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of mRNA catabolic process / negative regulation of low-density lipoprotein particle clearance / ATF4 activates genes in response to endoplasmic reticulum stress / 3'-UTR-mediated mRNA destabilization / negative regulation of nitric oxide biosynthetic process / miRNA metabolic process / mRNA 3'-UTR AU-rich region binding / RNA splicing, via transesterification reactions / KSRP (KHSRP) binds and destabilizes mRNA / cellular response to cytokine stimulus ...positive regulation of mRNA catabolic process / negative regulation of low-density lipoprotein particle clearance / ATF4 activates genes in response to endoplasmic reticulum stress / 3'-UTR-mediated mRNA destabilization / negative regulation of nitric oxide biosynthetic process / miRNA metabolic process / mRNA 3'-UTR AU-rich region binding / RNA splicing, via transesterification reactions / KSRP (KHSRP) binds and destabilizes mRNA / cellular response to cytokine stimulus / mRNA transport / regulation of mRNA stability / protein folding chaperone / RNA splicing / mRNA processing / mRNA binding / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / Far upstream element-binding protein, C-terminal / Far upstream element-binding protein, C-terminal / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 ...: / : / : / : / Far upstream element-binding protein, C-terminal / Far upstream element-binding protein, C-terminal / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Far upstream element-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / ARIA
AuthorsNicastro, G. / Garcia-Mayoral, M.F. / Hollingworth, D. / Kelly, G. / Martin, S.R. / Briata, P. / Gherzi, R. / Ramos, A.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Noncanonical G Recognition Mediates Ksrp Regulation of Let-7 Biogenesis
Authors: Nicastro, G. / Garcia-Mayoral, M.F. / Hollingworth, D. / Kelly, G. / Martin, S.R. / Briata, P. / Gherzi, R. / Ramos, A.
#1: Journal: Structure / Year: 2007
Title: The Structure of the C-Terminal Kh Domains of Ksrp Reveals a Noncanonical Motif Important for Mrna Degradation.
Authors: Garcia-Mayoral, M.F. / Hollingworth, D. / Masino, L. / Diaz-Moreno, I. / Kelly, G. / Gherzi, R. / Chou, C. / Chen, C. / Ramos, A.
History
DepositionAug 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Other / Structure summary
Revision 1.3Dec 5, 2012Group: Atomic model
Revision 1.4Jan 16, 2013Group: Database references
Revision 1.5May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KH-TYPE SPLICING REGULATORY PROTEIN
B: 5'-R(*AP*GP*GP*GP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)12,5392
Polymers12,5392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1

-
Components

#1: Protein KH-TYPE SPLICING REGULATORY PROTEIN


Mass: 10912.468 Da / Num. of mol.: 1 / Fragment: THIRD KH DOMAIN, RESIDUES 317-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q92945
#2: RNA chain 5'-R(*AP*GP*GP*GP*UP)-3'


Mass: 1626.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

-
Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 100 MM NACL / pH: 7.4 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
UXNMR3.5structure solution
VNMRstructure solution
NMRPipestructure solution
Sparkystructure solution
ARIA1.2structure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
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://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