[English] 日本語
Yorodumi
- PDB-1vol: TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vol
TitleTFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY COMPLEX
Components
  • DNA (5'-D(*CP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*G)-3')
  • PROTEIN (TATA BINDING PROTEIN (TBP))
  • PROTEIN (TRANSCRIPTION FACTOR IIB (TFIIB))
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION INITIATION / MOLECULAR RECOGNITION / COMPLEX / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION / DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / protein acetylation ...positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / protein acetylation / cell division site / acetyltransferase activity / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / viral transcription / RNA polymerase II complex binding / RNA polymerase II transcribes snRNA genes / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / spindle assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / DNA-templated transcription initiation / protein-DNA complex / kinetochore / RNA polymerase II transcription regulator complex / chromosome / DNA-binding transcription factor binding / transcription by RNA polymerase II / nuclear body / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding ...TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Cyclin A; domain 1 / TBP domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein 1 / Transcription initiation factor IIB
Similarity search - Component
Biological speciesHomo sapiens (human)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsNikolov, D.B. / Chen, H. / Halay, E.D. / Usheva, A.U. / Hisatake, K. / Lee, D.K. / Roeder, R.G. / Burley, S.K.
CitationJournal: Nature / Year: 1995
Title: Crystal structure of a TFIIB-TBP-TATA-element ternary complex.
Authors: Nikolov, D.B. / Chen, H. / Halay, E.D. / Usheva, A.A. / Hisatake, K. / Lee, D.K. / Roeder, R.G. / Burley, S.K.
History
DepositionApr 29, 1996Processing site: NDB
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*G)-3')
D: DNA (5'-D(*CP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*C)-3')
A: PROTEIN (TRANSCRIPTION FACTOR IIB (TFIIB))
B: PROTEIN (TATA BINDING PROTEIN (TBP))


Theoretical massNumber of molelcules
Total (without water)54,9644
Polymers54,9644
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)69.900, 78.000, 134.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 4987.253 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*C)-3')


Mass: 4809.129 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TRANSCRIPTION FACTOR IIB (TFIIB))


Mass: 22767.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403
#4: Protein PROTEIN (TATA BINDING PROTEIN (TBP))


Mass: 22400.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P28147

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3-0.4 mMDNA complex1drop
240 mM1dropKCl
3300 mMammonium acetate1drop
45 mM1dropMgCl2
55 mM1dropCaCl2
60.01 mMzinc acetate1drop
710 mMdithiothreitol1drop
810 %(v/v)glycerol1drop
940 mMTris-HCl1drop
105-10 %(v/v)glycerol1reservoir
1120 mMdithiothreitol1reservoir
1240 mMTris-HCl1reservoir
132 %(v/v)ethylene glycerol1drop

-
Data collection

DiffractionMean temperature: 123 K
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 20995 / % possible obs: 82.1 % / Rsym value: 0.072
Reflection
*PLUS
Highest resolution: 2.7 Å / % possible obs: 82.1 % / Num. measured all: 180515 / Rmerge(I) obs: 0.072

-
Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→8 Å
RfactorNum. reflection
Rfree0.318 1619
Rwork0.215 -
obs0.215 14676
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 650 0 0 3716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.86
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å
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://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