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- PDB-1nh2: Crystal structure of a yeast TFIIA/TBP/DNA complex -

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Basic information

Entry
Database: PDB / ID: 1nh2
TitleCrystal structure of a yeast TFIIA/TBP/DNA complex
Components
  • (Transcription initiation factor ...) x 4
  • 5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3'
  • 5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU)P*AP*AP*AP*AP*C)-3'
KeywordsTRANSCRIPTION/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 / 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 / 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 / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / 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 / 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-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 / 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: 1.9 Å
AuthorsBleichenbacher, M. / Tan, S. / Richmond, T.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes.
Authors: Bleichenbacher, M. / Tan, S. / Richmond, T.J.
History
DepositionDec 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU)P*AP*AP*AP*AP*C)-3'
F: 5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3'
A: Transcription initiation factor TFIID
B: Transcription initiation factor IIA large chain
C: Transcription initiation factor IIA large chain
D: Transcription initiation factor IIA small chain


Theoretical massNumber of molelcules
Total (without water)58,5296
Polymers58,5296
Non-polymers00
Water8,593477
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.010, 92.020, 117.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules EF

#1: DNA chain 5'-D(*TP*GP*TP*AP*(5IU)P*GP*TP*AP*TP*AP*(5IU)P*AP*AP*AP*AP*C)-3'


Mass: 5143.980 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3'


Mass: 4871.202 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Transcription initiation factor ... , 4 types, 4 molecules ABCD

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


Mass: 20120.754 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 180 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPT15 OR BTF1 OR YER148W / Production host: Escherichia coli (E. coli) / References: UniProt: P13393
#4: Protein Transcription initiation factor IIA large chain / TFIIA 32 kDa subunit


Mass: 6135.750 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 54 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOA1 OR YOR194C / Production host: Escherichia coli (E. coli) / References: UniProt: P32773
#5: Protein Transcription initiation factor IIA large chain / TFIIA 32 kDa subunit


Mass: 8915.654 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 77 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOA1 OR YOR194C / Production host: Escherichia coli (E. coli) / References: UniProt: P32774, UniProt: P32773*PLUS
#6: Protein Transcription initiation factor IIA small chain / TFIIA 13.5 kDa subunit


Mass: 13341.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOA2 OR YKL058W / Production host: Escherichia coli (E. coli) / References: UniProt: P32773, UniProt: P32774*PLUS

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Non-polymers , 1 types, 477 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
22 mMBis-Tris1droppH7.0
320 mM1dropKCl
40.1 mMEDTA1drop
50.5 mMdithiothreitol1drop
60.01 %(w/v)1dropNaN3
750 mMbis-Tris1reservoirpH6.5
8100 mM1reservoirLiNO3
910 mM1reservoirCaCl2
101 mMdithiothreitol1reservoir
1112 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 217906 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.3 Å2
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 48353 / % possible obs: 94.9 % / Redundancy: 4.5 % / Num. measured all: 217906 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / % possible obs: 98.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.147

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.93 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4843 10 %RANDOM, EXPANDED FROM 1YTF
Rwork0.201 ---
all0.204 ---
obs0.201 48353 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.6007 Å2 / ksol: 0.460095 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.74 Å20 Å20 Å2
2---5.1 Å20 Å2
3----0.64 Å2
Refine analyzeLuzzati coordinate error free: 0.23 Å / Luzzati sigma a free: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 650 0 477 4204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.963
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.231 613 9.9 %
Rwork0.198 5580 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor Rfree: 0.236 / Rfactor Rwork: 0.205

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