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- PDB-1tgh: TATA BINDING PROTEIN (TBP)/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1tgh
TitleTATA BINDING PROTEIN (TBP)/DNA COMPLEX
Components
  • DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*G)-3')
  • PROTEIN (TATA BINDING PROTEIN (TBP))
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / DNA BINDING PROTEIN / DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIA complex / RNA Polymerase III Abortive And Retractive Initiation / female germ cell nucleus / male pronucleus ...RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIA complex / RNA Polymerase III Abortive And Retractive Initiation / female germ cell nucleus / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / RNA Polymerase I Transcription Termination / 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 / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / male germ cell nucleus / SIRT1 negatively regulates rRNA expression / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / euchromatin / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA-binding transcription factor binding / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / Estrogen-dependent gene expression / transcription by RNA polymerase II / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / enzyme binding / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
TATA-Binding Protein / 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. / TBP domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsJuo, Z.S. / Dickerson, R.E.
Citation
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: 1.9 A Resolution Refined Structure of TBP Recognizing the Minor Groove of TATAAAAG
Authors: Kim, J.L. / Burley, S.K.
#2: Journal: Nature / Year: 1993
Title: Co-Crystal Structure of TBP Recognizing the Minor Groove of a TATA Element
Authors: Kim, J.L. / Nikolov, D.B. / Burley, S.K.
History
DepositionFeb 13, 1996Processing site: NDB
Revision 1.0Aug 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,1243
Polymers28,1243
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.965, 67.397, 86.226
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(*CP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*G)-3')


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (TATA BINDING PROTEIN (TBP)) / HTBP


Mass: 20801.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP / Plasmid: PET21D / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P20226
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 55 %
Crystal growpH: 8 / Details: pH 8.00
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.6 mMhTBPc and DNA1drop
220 mMTris-HCl1drop
3350 mMammonium acetate1drop
410 %(v/v)glycerol1drop
55 mMDTT1drop
61 mM1dropNaN3
720 mMTris-HCl1reservoir
8350 mMammonium acetate1reservoir
910 %(v/v)glycerol1reservoir
105 mMDTT1reservoir
111 mM1reservoirNaN3
125 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 92 K
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 19, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→50 Å / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. obs: 9013

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.294 -10 %
Rwork0.214 --
obs-9013 -
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 534 0 54 2355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Rfactor obs: 0.2145 / Rfactor Rfree: 0.2946 / Rfactor Rwork: 0.2145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.141 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.0004
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.533
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4926

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