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- PDB-4b0a: The high-resolution structure of yTBP-yTAF1 identifies conserved ... -

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Basic information

Entry
Database: PDB / ID: 4b0a
TitleThe high-resolution structure of yTBP-yTAF1 identifies conserved and competing interaction surfaces in transcriptional activation
ComponentsTRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1, LINKER, TATA-BOX-BINDING PROTEIN
KeywordsTRANSCRIPTION
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 / RNA polymerase II general transcription initiation factor binding / DNA binding, bending ...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 / RNA polymerase II general transcription initiation factor binding / 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 / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / 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 / transcription by RNA polymerase II / molecular adaptor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
TATA-Binding Protein / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site ...TATA-Binding Protein / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TATA-box-binding protein / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsAnandapadamanaban, M. / Andresen, C. / Siponen, M. / Kokubo, T. / Ikura, M. / Moche, M. / Sunnerhagen, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: High-Resolution Structure of TBP with Taf1 Reveals Anchoring Patterns in Transcriptional Regulation
Authors: Anandapadamanaban, M. / Andresen, C. / Siponen, M. / Kokubo, T. / Ikura, M. / Moche, M. / Sunnerhagen, M.
History
DepositionJun 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 21, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1, LINKER, TATA-BOX-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,02511
Polymers30,3161
Non-polymers70810
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.894, 74.253, 99.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1, LINKER, TATA-BOX-BINDING PROTEIN / TATA SEQUENCE-BINDING PROTEIN / TBP / TATA-BINDING FACTOR / TATA-BOX FACTOR / TRANSCRIPTION FACTOR ...TATA SEQUENCE-BINDING PROTEIN / TBP / TATA-BINDING FACTOR / TATA-BOX FACTOR / TRANSCRIPTION FACTOR D / TRANSCRIPTION INITIATION FACTOR TFIID TBP SUBUNIT / TAFII-130 / TAFII-145 / TBP-ASSOCIATED FACTOR 1 / TBP-ASSOCIATED FACTOR 145 KDA


Mass: 30316.363 Da / Num. of mol.: 1 / Fragment: TAF1 RESIDUES 8-71, LINKER, TBP RESIDUE 61-240 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS
References: UniProt: P46677, UniProt: P13393, histone acetyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ENTRY CONTAINS AN ENGINEERED FUSION PROTEIN. THE TAND1 AND TAND2 REGION (8-71) OF TAF1 IS ...THE ENTRY CONTAINS AN ENGINEERED FUSION PROTEIN. THE TAND1 AND TAND2 REGION (8-71) OF TAF1 IS COVALENTLY LINKED VIA A PROTEIN LINKER (GGGSGGGSGGGS) TO TBP (61-240) IN ORDER TO ACCOMMODATE THESE IN THE SAME PDB CHAIN AN OFFSET OF 100 HAS BEEN APPLIED TO THE TBP RESIDUE NUMBERING AND SO THIS NOW RUNS FROM 161 TO 340 RATHER THAN 61 TO 240. OTHER_DETAILS: CONSTRUCTS CONTAIN RESIDUE: 8-71 MUTATIONS: G41A AND A42R, WHICH ARE DUE TO A CLONING ARTIFACT, RELATIVE TO THE UNIPROT ENTRY: P46677

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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: 2.01 Å3/Da / Density % sol: 38.73 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.97→59.54 Å / Num. obs: 17942 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 25.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.3
Reflection shellResolution: 1.97→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YTB

1ytb


Resolution: 1.97→59.54 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.9188 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.154
Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL CA GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2149. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL CA GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2149. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=37. NUMBER TREATED BY BAD NON- BONDED CONTACTS=3.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 888 4.97 %RANDOM
Rwork0.1644 ---
obs0.167 17873 99.36 %-
Displacement parametersBiso mean: 28.39 Å2
Baniso -1Baniso -2Baniso -3
1--3.2727 Å20 Å20 Å2
2--2.589 Å20 Å2
3---0.6836 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.97→59.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 40 213 2104
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012008HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022710HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d949SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes295HARMONIC5
X-RAY DIFFRACTIONt_it2008HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion2.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion262SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2561SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.09 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.221 127 4.53 %
Rwork0.1851 2678 -
all0.1868 2805 -
obs--99.36 %

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