[English] 日本語
Yorodumi
- SASDD75: 'TG'-interacting factor homeodomain in solution (Homeobox protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDD75
Sample'TG'-interacting factor homeodomain in solution (Homeobox protein TGIF1)
  • Homeobox protein TGIF1 (protein), TGIF, Homo sapiens
Function / homology
Function and homology information


co-SMAD binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to growth factor stimulus / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity ...co-SMAD binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to growth factor stimulus / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Homeobox KN domain / Homeobox KN domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeobox protein TGIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Contact author
  • Ewelina Guca (Institute for Research in Biomedicine in Barcelona)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1826
Type: dummy / Radius of dummy atoms: 2.25 A / Symmetry: P1 / Chi-square value: 1.123 / P-value: 0.657170
Search similar-shape structures of this assembly by Omokage search (details)
Model #1828
Type: atomic / Symmetry: P1
Comment: Two monomers (B) and (D) have been used as rigid bodies and N- and C-terminal loops were modelled.
Chi-square value: 1.721
Search similar-shape structures of this assembly by Omokage search (details)
Model #1833
Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 1.116 / P-value: 0.198541
Search similar-shape structures of this assembly by Omokage search (details)
Model #1835
Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 1.116 / P-value: 0.198541
Search similar-shape structures of this assembly by Omokage search (details)
Model #1836
Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 1.116 / P-value: 0.198541
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: 'TG'-interacting factor homeodomain in solution (Homeobox protein TGIF1)
Specimen concentration: 6 mg/ml
BufferName: 20 mM Tris, 150 mM NaCl / pH: 7.4
Entity #986Name: TGIF / Type: protein / Description: Homeobox protein TGIF1 / Formula weight: 10.68 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q15583
Sequence:
GPDIPLDLSS SAGSGKRRRR GNLPKESVQI LRDWLYEHRY NAYPSEQEKA LLSQQTHLST LQVCNWFINA RRRLLPDMLR KDGKDPNQFT IS

-
Experimental information

BeamInstrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 1.5 mm
DetectorName: Pilatus 2M
Scan
Title: 'TG'-interacting factor homeodomain in solution (Homeobox protein TGIF1)
Measurement date: Oct 18, 2016 / Storage temperature: 10 °C / Cell temperature: 20 °C / Exposure time: 0.045 sec. / Number of frames: 120 / Unit: 1/nm /
MinMax
Q0.095 7.9013
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 545 /
MinMax
Q0.0950367 2.95664
P(R) point1 545
R0 9.21
Result
Type of curve: single_conc /
ExperimentalPorod
MW25.5 kDa26 kDa
Volume-42 nm3

P(R)GuinierGuinier error
Forward scattering, I011350 11423.2 73.9
Radius of gyration, Rg2.753 nm2.7 nm0.05

MinMax
D-9.21
Guinier point1 74

+
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