[English] 日本語
Yorodumi
- SASDAR4: PTB full (Polypyrimidine tract-binding protein 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDAR4
SamplePTB full
  • Polypyrimidine tract-binding protein 1 (protein), Homo sapiens
Function / homology
Function and homology information


negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of cell differentiation / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome ...negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of cell differentiation / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of protein dephosphorylation / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP 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
Similarity search - Domain/homology
Polypyrimidine tract-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationJournal: Structure / Year: 2006
Title: Conformation of polypyrimidine tract binding protein in solution.
Authors: Maxim V Petoukhov / Tom P Monie / Frédéric H-T Allain / Stephen Matthews / Stephen Curry / Dmitri I Svergun /
Abstract: The polypyrimidine tract binding protein (PTB) is an RNA binding protein that normally functions as a regulator of alternative splicing but can also be recruited to stimulate translation initiation ...The polypyrimidine tract binding protein (PTB) is an RNA binding protein that normally functions as a regulator of alternative splicing but can also be recruited to stimulate translation initiation by certain picornaviruses. High-resolution structures of the four RNA recognition motifs (RRMs) that make up PTB have previously been determined by NMR. Here, we have used small-angle X-ray scattering to determine the low-resolution structure of the entire protein. Scattering patterns from full-length PTB and deletion mutants containing all possible sequential combinations of the RRMs were collected. All constructs were found to be monomeric in solution. Ab initio analysis and rigid-body modeling utilizing the high-resolution models of the RRMs yielded a consistent low-resolution model of the spatial organization of domains in PTB. Domains 3 and 4 were found to be in close contact, whereas domains 2 and especially 1 had loose contacts with the rest of the protein.
Contact author
  • Maxim Petoukhov (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #76
Type: mix / Software: Bunch / Radius of dummy atoms: 1.90 A / Chi-square value: 1.1664
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: PTB full / Sample MW: 57.22 kDa / Specimen concentration: 6.40-20.40
BufferName: 25 mM Tris / pH: 7.2 / Composition: 100 mM NaCl, 5.0 mM DTT
Entity #65Type: protein / Description: Polypyrimidine tract-binding protein 1 / Formula weight: 57.22 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P26599
Sequence: MDGIVPDIAV GTKRGSDELF STCVTNGPFI MSSNSASAAN GNDSKKFKGD SRSAGVPSRV IHIRKLPIDV TEGEVISLGL PFGKVTNLLM LKGKNQAFIE MNTEEAANTM VNYYTSVTPV LRGQPIYIQF SNHKELKTDS SPNQARAQAA LQAVNSVQSG NLALAASAAA ...Sequence:
MDGIVPDIAV GTKRGSDELF STCVTNGPFI MSSNSASAAN GNDSKKFKGD SRSAGVPSRV IHIRKLPIDV TEGEVISLGL PFGKVTNLLM LKGKNQAFIE MNTEEAANTM VNYYTSVTPV LRGQPIYIQF SNHKELKTDS SPNQARAQAA LQAVNSVQSG NLALAASAAA VDAGMAMAGQ SPVLRIIVEN LFYPVTLDVL HQIFSKFGTV LKIITFTKNN QFQALLQYAD PVSAQHAKLS LDGQNIYNAC CTLRIDFSKL TSLNVKYNND KSRDYTRPDL PSGDSQPSLD QTMAAAFGLS VPNVHGALAP LAIPSAAAAA AAAGRIAIPG LAGAGNSVLL VSNLNPERVT PQSLFILFGV YGDVQRVKIL FNKKENALVQ MADGNQAQLA MSHLNGHKLH GKPIRITLSK HQNVQLPREG QEDQGLTKDY GNSPLHRFKK PGSKNFQNIF PPSATLHLSN IPPSVSEEDL KVLFSSNGGV VKGFKFFQKD RKMALIQMGS VEEAVQALID LHNHDLGENH HLRVSFSKST I

-
Experimental information

BeamInstrument name: DORIS III X33 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron
DetectorName: 1D Gas detector
Scan
Title: PTB full / Measurement date: Feb 11, 2004 / Unit: 1/nm /
MinMax
Q0.1441 3.2532
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 355 /
MinMax
Q0.01551 0.2012
P(R) point2 356
R0 165
Result
Experimental MW: 60 kDa / Type of curve: merged
GuinierP(R)
Forward scattering, I0206 -
Radius of gyration, Rg3.97 nm4.4 nm

MinMax
D-16.5
Guinier point2 17

+
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