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- PDB-1ytb: CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ytb
TitleCRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX
Components
  • DNA (29MER)
  • PROTEIN (TATA BINDING PROTEIN (TBP))
KeywordsTRANSCRIPTION/DNA / PROTEIN-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 / 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 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 general transcription initiation factor activity / transcription factor TFIID complex / 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 / DNA-binding transcription factor binding / transcription regulator complex / 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
DNA / DNA (> 10) / TATA-box-binding protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKim, Y. / Geiger, J.H. / Hahn, S. / Sigler, P.B.
CitationJournal: Nature / Year: 1993
Title: Crystal structure of a yeast TBP/TATA-box complex.
Authors: Kim, Y. / Geiger, J.H. / Hahn, S. / Sigler, P.B.
History
DepositionSep 28, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 26, 1995Provider: 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (29MER)
D: DNA (29MER)
A: PROTEIN (TATA BINDING PROTEIN (TBP))
B: PROTEIN (TATA BINDING PROTEIN (TBP))


Theoretical massNumber of molelcules
Total (without water)58,2174
Polymers58,2174
Non-polymers00
Water9,242513
1
C: DNA (29MER)
A: PROTEIN (TATA BINDING PROTEIN (TBP))


Theoretical massNumber of molelcules
Total (without water)29,1092
Polymers29,1092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA (29MER)
B: PROTEIN (TATA BINDING PROTEIN (TBP))


Theoretical massNumber of molelcules
Total (without water)29,1092
Polymers29,1092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.770, 100.770, 66.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
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: (-0.06319, -0.9977, 0.0237), (-0.9939, 0.06077, -0.09169), (0.09004, -0.02935, -0.9955)
Vector: 49.65, 55.11, 66.59)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 61 - A 240 B 61 - B 240 0.445 M1 C 1 - C 29 D 1 - D 29 1.571

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Components

#1: DNA chain DNA (29MER)


Mass: 8987.817 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (TATA BINDING PROTEIN (TBP))


Mass: 20120.754 Da / Num. of mol.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 800011
3GLYCEROL11
4ETHYLENE GLYCOL11
5NACL11
6BIS-TRIS-PROPANE_HCL11
7WATER12
8PEG 800012
9GLYCEROL12
10ETHYLENE GLYCOL12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.25 mMprotein1drop
20.5 mMDNA1drop
3500 mM1dropNaCl
420 mM1,3-bis(tris-(hydroxymethyl)-methylamino) propane1drop
515 %PEG80001drop
61 %ethylene glycol1drop
730 %PEG80001reservoir
840 mM1,3-bis(tris-(hydroxymethyl)-methylamino) propane1reservoir
92.5 %glycerol1reservoir
102 %ethylene glycol1reservoir
11500 mM1reservoirNaCl

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 59705 / % possible obs: 98.5 %
Reflection
*PLUS
% possible obs: 98.5 %

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.8→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.261 --
Rwork0.201 --
obs0.201 51009 86.7 %
Displacement parametersBiso mean: 35.1 Å2
Refine analyzeLuzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 1194 0 513 4539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d31.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
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: 1.8 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.201 / Rfactor Rfree: 0.261
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.1 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.56

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