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- PDB-1rm1: Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex -

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Basic information

Entry
Database: PDB / ID: 1rm1
TitleStructure of a Yeast TFIIA/TBP/TATA-box DNA Complex
Components
  • (Transcription initiation factor IIA ...) x 2
  • 5'-D(*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*AP*TP*AP*AP*AP*AP*CP*G)-3'
  • 5'-D(P*CP*GP*TP*TP*TP*TP*AP*TP*AP*TP*CP*GP*AP*TP*CP*GP*AP*T)-3'
  • TATA-box binding protein
KeywordsTRANSCRIPTION/DNA / Yeast TFIIA / TBP protein / ATA-box DNA / 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 / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / 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 / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / 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 Pre-transcription Events / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / disordered domain specific binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Helix Hairpins - #100 / TATA-Binding Protein / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain ...Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Helix Hairpins - #100 / TATA-Binding Protein / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / 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 / Helix Hairpins / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJin, X. / Gewirth, D.T. / Geiger, J.H.
CitationJournal: TO BE PUBLISHED
Title: High Resolution Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex
Authors: Jin, X. / Gewirth, D.T. / Geiger, J.H.
History
DepositionNov 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
D: 5'-D(*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*AP*TP*AP*AP*AP*AP*CP*G)-3'
E: 5'-D(P*CP*GP*TP*TP*TP*TP*AP*TP*AP*TP*CP*GP*AP*TP*CP*GP*AP*T)-3'
A: TATA-box binding protein
B: Transcription initiation factor IIA small chain
C: Transcription initiation factor IIA large chain


Theoretical massNumber of molelcules
Total (without water)83,7755
Polymers83,7755
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.250, 173.250, 164.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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DNA chain , 2 types, 2 molecules DE

#1: DNA chain 5'-D(*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*AP*TP*AP*AP*AP*AP*CP*G)-3'


Mass: 5532.631 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*CP*GP*TP*TP*TP*TP*AP*TP*AP*TP*CP*GP*AP*TP*CP*GP*AP*T)-3'


Mass: 5496.575 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Transcription initiation factor IIA ... , 2 types, 2 molecules BC

#4: Protein Transcription initiation factor IIA small chain / TFIIA 13.5 kDa subunit


Mass: 13473.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOA2, YKL058W / Production host: Escherichia coli (E. coli) / References: UniProt: P32774
#5: Protein Transcription initiation factor IIA large chain / TFIIA 32 kDa subunit


Mass: 32230.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOA1, YOR194C / Production host: Escherichia coli (E. coli) / References: UniProt: P32773

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Protein / Non-polymers , 2 types, 302 molecules A

#3: Protein TATA-box binding protein / TATA-box factor / TATA binding factor / TATA sequence-binding protein / TBP / Transcription factor ...TATA-box factor / TATA binding factor / TATA sequence-binding protein / TBP / Transcription factor D / Transcription initiation factor TFIID TBP subunit


Mass: 27042.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPT15, BTF1, YER148W / Production host: Escherichia coli (E. coli) / References: UniProt: P13393
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium citrate, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium citrate11
3MES11
4H2O11
5PEG 400012
6ammonium citrate12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.908 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Sep 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29228

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YTB

1ytb


Resolution: 2.5→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.252 2992 RANDOM
Rwork0.186 --
all0.201 32744 -
obs0.189 29188 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 735 0 301 4200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2

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