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- PDB-1tbp: CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INT... -

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Basic information

Entry
Database: PDB / ID: 1tbp
TitleCRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INTERACTION WITH DNA
ComponentsTATA-BINDING PROTEIN
KeywordsBINDING PROTEIN
Function / homology
Function and homology information


TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / 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 / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / 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 general transcription initiation factor activity / transcription factor TFIID complex / 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 / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / DNA-templated transcription initiation / disordered domain specific binding / transcription regulator complex / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus
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
TATA-box-binding protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsChasman, D.I. / Flaherty, K.M. / Sharp, P.A. / Kornberg, R.D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal structure of yeast TATA-binding protein and model for interaction with DNA.
Authors: Chasman, D.I. / Flaherty, K.M. / Sharp, P.A. / Kornberg, R.D.
#1: Journal: Nature / Year: 1992
Title: Crystal Structure of TFIID TATA-Box Binding Protein
Authors: Nikolov, D.B. / Hu, S.-H. / Lin, J. / Gasch, A. / Hoffmann, A. / Horikoshi, M. / Chua, N.-H. / Roeder, R.G. / Burley, S.K.
History
DepositionAug 2, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TATA-BINDING PROTEIN
B: TATA-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)40,3302
Polymers40,3302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-14 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.100, 104.100, 75.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO A 109 / 2: CIS PROLINE - PRO A 200 / 3: CIS PROLINE - PRO B 109 / 4: CIS PROLINE - PRO B 200
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.846596, -0.25936, 0.464766), (-0.380406, -0.315877, -0.869203), (0.372245, -0.912663, 0.168758)
Vector: 126.6754, 15.3731, -33.6987)

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Components

#1: Protein TATA-BINDING PROTEIN


Mass: 20164.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P13393

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal grow
*PLUS
pH: 7.25 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.002-0.005 mMprotein1drop
2800 mMsodium potassium phosphate1reservoir
3750 mM1reservoirNaCl
40.5 %(v/v)PEG4001reservoir
51 mMdithiothreitol1reservoir

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→6 Å / Rfactor Rwork: 0.211 / Rfactor obs: 0.211
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 0 0 2834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.64
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: 2.6 Å / Lowest resolution: 6 Å / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.64

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