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- PDB-1vol: TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY C... -

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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 / protein acetylation / cell division site / RNA polymerase II general transcription initiation factor activity ...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 / protein acetylation / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 / acetyltransferase activity / RNA polymerase II complex binding / viral transcription / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / RNA polymerase II preinitiation complex assembly / spindle assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / promoter-specific chromatin binding / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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