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- PDB-1ngm: Crystal structure of a yeast Brf1-TBP-DNA ternary complex -

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Basic information

Entry
Database: PDB / ID: 1ngm
TitleCrystal structure of a yeast Brf1-TBP-DNA ternary complex
Components
  • 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
  • 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
  • Transcription factor IIIB BRF1 subunit
  • Transcription initiation factor TFIID
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION / TFIIIB / TBP / BRF / BRF1 / TAF / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RNA polymerase III core binding / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity ...RNA polymerase III core binding / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity / regulation of transcription by RNA polymerase III / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / 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 Pre-transcription Events / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / disordered domain specific binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Single helix bin / Brf1, TBP-binding domain / Brf1-like TBP-binding domain / 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. ...Single helix bin / Brf1, TBP-binding domain / Brf1-like TBP-binding domain / 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. / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / 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. / TBP domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Transcription factor IIIB 70 kDa subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å
AuthorsJuo, Z.S. / Kassavetis, G.A. / Wang, J. / Geiduschek, E.P. / Sigler, P.B.
CitationJournal: Nature / Year: 2003
Title: Crystal structure of a transcription factor IIIB core interface ternary complex
Authors: Juo, Z.S. / Kassavetis, G.A. / Wang, J. / Geiduschek, E.P. / Sigler, P.B.
History
DepositionDec 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
C: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
G: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
H: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
K: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
L: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
O: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
P: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
A: Transcription initiation factor TFIID
B: Transcription factor IIIB BRF1 subunit
E: Transcription initiation factor TFIID
F: Transcription factor IIIB BRF1 subunit
I: Transcription initiation factor TFIID
J: Transcription factor IIIB BRF1 subunit
M: Transcription initiation factor TFIID
N: Transcription factor IIIB BRF1 subunit


Theoretical massNumber of molelcules
Total (without water)160,40216
Polymers160,40216
Non-polymers00
Water00
1
C: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
D: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
A: Transcription initiation factor TFIID
B: Transcription factor IIIB BRF1 subunit


Theoretical massNumber of molelcules
Total (without water)40,1014
Polymers40,1014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
H: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
E: Transcription initiation factor TFIID
F: Transcription factor IIIB BRF1 subunit


Theoretical massNumber of molelcules
Total (without water)40,1014
Polymers40,1014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
L: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
I: Transcription initiation factor TFIID
J: Transcription factor IIIB BRF1 subunit


Theoretical massNumber of molelcules
Total (without water)40,1014
Polymers40,1014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: 5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'
P: 5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'
M: Transcription initiation factor TFIID
N: Transcription factor IIIB BRF1 subunit


Theoretical massNumber of molelcules
Total (without water)40,1014
Polymers40,1014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.610, 152.600, 256.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain
5'-D(*CP*TP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*GP*TP*TP*TP*TP*TP*T)-3'


Mass: 5816.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: yeast U6 promoter TATA element
#2: DNA chain
5'-D(*AP*AP*AP*AP*AP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*G)-3'


Mass: 5825.834 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: yeast U6 promoter TATA element
#3: Protein
Transcription initiation factor TFIID / TATA-box factor / TATA sequence-binding protein / TBP / Transcription factor D


Mass: 20120.754 Da / Num. of mol.: 4 / Fragment: C-terminal core domain
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
#4: Protein
Transcription factor IIIB BRF1 subunit / BRF / TFIIB-related factor


Mass: 8337.169 Da / Num. of mol.: 4 / Fragment: Homology domain II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P29056

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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: 6.06 Å3/Da / Density % sol: 79.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, NaCl, BME, glycerol, MgCl2, PEG2000MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2NaCl11
3BME11
4glycerol11
5MgCl211
6PEG2000MME11
8NaCl12
11MgCl212
Crystal grow
*PLUS
Temperature: 4. ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mM1reservoirpH6.5
2100 mM1reservoiror LiClNaCl
310 mM1reservoirMgCl2
42 mM2-mercaptoethanol1reservoir
525 %(v/v)glycerol1reservoir
610 %(v/v)PEG2000 MME1reservoir
81
111

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.100, 0.919425, 0.918969
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.9194251
30.9189691
ReflectionResolution: 2.95→50 Å / Num. all: 78423 / Num. obs: 74659 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 62.39 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.95→3.06 Å / % possible all: 87
Reflection
*PLUS
Num. obs: 74859 / % possible obs: 95.5 % / Num. measured all: 269787

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.95→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Authors used CNS prior to the final refinement with REFMAC
RfactorNum. reflectionSelection details
Rfree0.308 3756 RANDOM
Rwork0.276 --
all0.278 70826 -
obs0.278 70826 -
Displacement parametersBiso mean: 29.23 Å2
Baniso -1Baniso -2Baniso -3
1-12.39 Å20 Å20 Å2
2---6.01 Å20 Å2
3----6.38 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7708 3092 0 0 10800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.441
Refinement
*PLUS
Lowest resolution: 48.5 Å / Num. reflection obs: 74582 / Rfactor Rwork: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.441

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