[English] 日本語
Yorodumi
- PDB-1ytf: YEAST TFIIA/TBP/DNA COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ytf
TitleYEAST TFIIA/TBP/DNA COMPLEX
Components
  • (PROTEIN (TRANSCRIPTION FACTOR IIA - ...) x 3
  • DNA (5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*AP*TP*GP*TP*AP*TP*AP*TP*AP*AP*AP*AP*C)-3')
  • PROTEIN (TATA BINDING PROTEIN (TBP))
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA / COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase III / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter ...TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase III / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / disordered domain specific binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Helix Hairpins - #100 / TATA-Binding Protein / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain ...Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Helix Hairpins - #100 / TATA-Binding Protein / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / Helix Hairpins / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsTan, S. / Hunziker, Y. / Sargent, D.F. / Richmond, T.J.
CitationJournal: Nature / Year: 1996
Title: Crystal structure of a yeast TFIIA/TBP/DNA complex.
Authors: Tan, S. / Hunziker, Y. / Sargent, D.F. / Richmond, T.J.
History
DepositionApr 5, 1996Processing site: NDB
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: DNA (5'-D(*TP*GP*TP*AP*TP*GP*TP*AP*TP*AP*TP*AP*AP*AP*AP*C)-3')
F: DNA (5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3')
A: PROTEIN (TATA BINDING PROTEIN (TBP))
B: PROTEIN (TRANSCRIPTION FACTOR IIA - TOA1N SUBUNIT)
C: PROTEIN (TRANSCRIPTION FACTOR IIA - TOA1C SUBUNIT)
D: PROTEIN (TRANSCRIPTION FACTOR IIA - TOA2 SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)58,3056
Polymers58,3056
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.150, 93.050, 117.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 2 types, 2 molecules EF

#1: DNA chain DNA (5'-D(*TP*GP*TP*AP*TP*GP*TP*AP*TP*AP*TP*AP*AP*AP*AP*C)-3')


Mass: 4920.240 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3')


Mass: 4871.202 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Protein , 1 types, 1 molecules A

#3: Protein PROTEIN (TATA BINDING PROTEIN (TBP))


Mass: 20120.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P13393

-
PROTEIN (TRANSCRIPTION FACTOR IIA - ... , 3 types, 3 molecules BCD

#4: Protein PROTEIN (TRANSCRIPTION FACTOR IIA - TOA1N SUBUNIT)


Mass: 6135.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: RECONSTITUTED FROM 3 INDIVIDUALLY OVEREXPRESSED POLYPEPTIDES;
Production host: Escherichia coli (E. coli) / References: UniProt: P32773
#5: Protein PROTEIN (TRANSCRIPTION FACTOR IIA - TOA1C SUBUNIT)


Mass: 8915.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P32773
#6: Protein PROTEIN (TRANSCRIPTION FACTOR IIA - TOA2 SUBUNIT)


Mass: 13341.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P32774

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 45 %
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlcomplex1drop
225 mMsodium acetate1reservoir
3100 mM1reservoirNH4Cl
410 mM1reservoirCaCl2
51 mMdithiothreitol1reservoir
68-10 %PEG60001reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 11, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 22476 / % possible obs: 97.2 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 97.2 % / Num. measured all: 196513 / Rmerge(I) obs: 0.05

-
Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.297 -
Rwork0.235 -
obs0.235 20758
Displacement parametersBiso mean: 21.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 650 0 0 3605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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