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- PDB-1d3u: TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMP... -

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Basic information

Entry
Database: PDB / ID: 1d3u
TitleTATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI
Components
  • DNA 23-MER: BRE+TATA-BOX
  • DNA 24-MER: BRE+TATA-BOX
  • TATA-BINDING PROTEIN
  • TRANSCRIPTION INITIATION FACTOR IIB
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION / HYPERTHERMOPHILE / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


transcriptional start site selection at RNA polymerase II promoter / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / DNA-binding transcription factor activity / DNA binding / zinc ion binding
Similarity search - Function
Transcription initiation factor TFIIB, archaea / TATA-box binding protein, archaea / TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like ...Transcription initiation factor TFIIB, archaea / TATA-box binding protein, archaea / TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-Binding Protein / 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) / Transcription initiation factor IIB / TATA-box-binding protein
Similarity search - Component
Biological speciesPyrococcus woesei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsLittlefield, O. / Korkhin, Y. / Sigler, P.B.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The structural basis for the oriented assembly of a TBP/TFB/promoter complex.
Authors: Littlefield, O. / Korkhin, Y. / Sigler, P.B.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The orientation of the transcription preinitiation complex in Archaea
Authors: Bell, S.D. / Kosa, P.L. / Sigler, P.B. / Jackson, S.P.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The 2.1-angstrom crystal structure of an archaeal preinitiation complex: TATA- box-binding protein/transcription factor (II)B core/TATA-box
Authors: Kosa, P.F. / Ghosh, G. / DeDecker, B.S. / Sigler, P.B.
#3: Journal: Mol.Cell / Year: 1998
Title: Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength
Authors: Qureshi, S.A. / Jackson, S.P.
#4: Journal: Genes Dev. / Year: 1998
Title: New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB
Authors: Lagrange, T. / Kapanidis, A.N. / Tang, H. / Reinberg, D. / Ebright, R.H.
History
DepositionOct 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: 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
C: DNA 24-MER: BRE+TATA-BOX
D: DNA 23-MER: BRE+TATA-BOX
A: TATA-BINDING PROTEIN
B: TRANSCRIPTION INITIATION FACTOR IIB


Theoretical massNumber of molelcules
Total (without water)57,3074
Polymers57,3074
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.200, 174.200, 174.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Cell settingcubic
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-272-

HOH

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Components

#1: DNA chain DNA 24-MER: BRE+TATA-BOX


Mass: 7414.853 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA 23-MER: BRE+TATA-BOX


Mass: 7003.568 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein TATA-BINDING PROTEIN / TATA-BOX FACTOR / TATA SEQUENCE-BINDING PROTEIN / TBP


Mass: 20166.549 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus woesei (archaea) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P62001
#4: Protein TRANSCRIPTION INITIATION FACTOR IIB / TFIIB


Mass: 22721.576 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CORE, RESIDUES 62-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus woesei (archaea) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P61999
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, STRONTIUM CHLORIDE, SODIUM CITRATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1SRCL211
2SODIUM CITRATE11
3TRIS11
4PEG 40011
5PEG 40012
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.4 mMTBP1drop
20.4 mMTFB1drop
30.6 mMDNA1drop
4200 mMpotassium acetate1drop
550 mMHEPES1drop
630 %(w/v)PEG4001reservoir
725 mMSrCl21reservoir
8200 mMsodium citrate1reservoir
950 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.4→28.3 Å / Num. obs: 33982 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.339 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
CNSrefinement
HKL-2000data reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.245 3323 10 %
Rwork0.206 --
all0.212 33798 -
obs0.212 33798 98.7 %
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 957 0 180 4147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.6

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