[English] 日本語
Yorodumi
- SASDED2: Polyglutamine tract-binding protein 1 (PQBP-1) (Polyglutamine-bin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDED2
SamplePolyglutamine tract-binding protein 1 (PQBP-1)
  • Polyglutamine-binding protein 1 (protein), PQBP-1, Homo sapiens
Function / homology
Function and homology information


neuronal ribonucleoprotein granule / alternative mRNA splicing, via spliceosome / cellular response to exogenous dsRNA / regulation of dendrite morphogenesis / regulation of RNA splicing / positive regulation of type I interferon production / positive regulation of defense response to virus by host / ribonucleoprotein complex binding / activation of innate immune response / mRNA Splicing - Major Pathway ...neuronal ribonucleoprotein granule / alternative mRNA splicing, via spliceosome / cellular response to exogenous dsRNA / regulation of dendrite morphogenesis / regulation of RNA splicing / positive regulation of type I interferon production / positive regulation of defense response to virus by host / ribonucleoprotein complex binding / activation of innate immune response / mRNA Splicing - Major Pathway / cytoplasmic stress granule / neuron projection development / double-stranded DNA binding / defense response to virus / transcription coactivator activity / nuclear body / nuclear speck / innate immune response / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Polyglutamine-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationJournal: Biophys J / Year: 2012
Title: Solution model of the intrinsically disordered polyglutamine tract-binding protein-1.
Authors: Martin Rees / Christian Gorba / Cesira de Chiara / Tam T T Bui / Mitla Garcia-Maya / Alex F Drake / Hitoshi Okazawa / Annalisa Pastore / Dmitri Svergun / Yu Wai Chen /
Abstract: Polyglutamine tract-binding protein-1 (PQBP-1) is a 265-residue nuclear protein that is involved in transcriptional regulation. In addition to its role in the molecular pathology of the polyglutamine ...Polyglutamine tract-binding protein-1 (PQBP-1) is a 265-residue nuclear protein that is involved in transcriptional regulation. In addition to its role in the molecular pathology of the polyglutamine expansion diseases, mutations of the protein are associated with X-linked mental retardation. PQBP-1 binds specifically to glutamine repeat sequences and proline-rich regions, and interacts with RNA polymerase II and the spliceosomal protein U5-15kD. In this work, we obtained a biophysical characterization of this protein by employing complementary structural methods. PQBP-1 is shown to be a moderately compact but largely disordered molecule with an elongated shape, having a Stokes radius of 3.7 nm and a maximum molecular dimension of 13 nm. The protein is monomeric in solution, has residual β-structure, and is in a premolten globule state that is unaffected by natural osmolytes. Using small-angle x-ray scattering data, we were able to generate a low-resolution, three-dimensional model of PQBP-1.
Contact author
  • Yu Wai Chen (King's College London)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2194
Type: dummy / Software: (1.1.0 r980) / Radius of dummy atoms: 2.70 A / Chi-square value: 1.018081 / P-value: 0.058031
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Polyglutamine tract-binding protein 1 (PQBP-1) / Specimen concentration: 7.00-13.00
BufferName: 20 mM Tris, 150 mM NaCl, 1mM DTT, / pH: 7
Entity #1201Name: PQBP-1 / Type: protein / Description: Polyglutamine-binding protein 1 / Formula weight: 30.626 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: O60828
Sequence: GPMPLPVALQ TRLAKRGILK HLEPEPEEEI IAEDYDDDPV DYEATRLEGL PPSWYKVFDP SCGLPYYWNA DTDLVSWLSP HDPNSVVTKS AKKLRSSNAD AEEKLDRSHD KSDRGHDKSD RSHEKLDRGH DKSDRGHDKS DRDRERGYDK VDRERERDRE RDRDRGYDKA ...Sequence:
GPMPLPVALQ TRLAKRGILK HLEPEPEEEI IAEDYDDDPV DYEATRLEGL PPSWYKVFDP SCGLPYYWNA DTDLVSWLSP HDPNSVVTKS AKKLRSSNAD AEEKLDRSHD KSDRGHDKSD RSHEKLDRGH DKSDRGHDKS DRDRERGYDK VDRERERDRE RDRDRGYDKA DREEGKERRH HRREELAPYP KSKKAVSRKD EELDPMDPSS YSDAPRGTWS TGLPKRNEAK TGADTTAAGP LFQQRPYPSP GAVLRANAEA SRTKQQD

-
Experimental information

BeamInstrument name: DORIS III EMBL X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.7 mm
DetectorName: Pilatus 1M-W / Pixsize x: 0.172 mm
Scan
Title: Polyglutamine tract-binding protein 1 (PQBP-1) / Measurement date: Nov 18, 2009 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 15 sec. / Number of frames: 8 / Unit: 1/nm /
MinMax
Q0.0775 6.2077
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 500 /
MinMax
Q0.07879 2.741
P(R) point1 500
R0 13
Result
Type of curve: merged
ExperimentalStandardStandard errorPorod
MW30.6 kDa30 kDa3 35 kDa
Volume---51 nm3

P(R)GuinierGuinier error
Forward scattering, I040.75 40.49 -
Radius of gyration, Rg3.82 nm3.72 nm0.2

MinMax
D-13
Guinier point30 97

+
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