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- PDB-6ueq: Structure of TBP bound to C-C mismatch containing TATA site -

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Basic information

Entry
Database: PDB / ID: 6ueq
TitleStructure of TBP bound to C-C mismatch containing TATA site
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*CP*GP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
  • TATA-box-binding protein 1
KeywordsDNA BINDING PROTEIN/DNA / TBP / TATA box / transcription / NER / mismatch DNA site / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA binding / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSchumacher, M.A. / Al-Hashimi, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Nature / Year: 2020
Title: DNA mismatches reveal conformational penalties in protein-DNA recognition.
Authors: Afek, A. / Shi, H. / Rangadurai, A. / Sahay, H. / Senitzki, A. / Xhani, S. / Fang, M. / Salinas, R. / Mielko, Z. / Pufall, M.A. / Poon, G.M.K. / Haran, T.E. / Schumacher, M.A. / Al-Hashimi, H.M. / Gordan, R.
History
DepositionSep 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 4, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: TATA-box-binding protein 1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*CP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2265
Polymers33,0343
Non-polymers1922
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-42 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.403, 45.583, 155.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-421-

HOH

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Components

#1: Protein TATA-box-binding protein 1 / AtTBP1 / TATA sequence-binding protein 1 / TBP-1 / TATA-binding factor 1 / TATA-box factor 1 / ...AtTBP1 / TATA sequence-binding protein 1 / TBP-1 / TATA-binding factor 1 / TATA-box factor 1 / Transcription initiation factor TFIID TBP-1 subunit


Mass: 24514.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TBP1, At3g13445, MRP15.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P28147
#2: DNA chain DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*CP*GP*GP*CP*A)-3')


Mass: 4297.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Mass: 4221.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: sodium acetate pH 4.5, 28% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→155.2 Å / Num. obs: 12803 / % possible obs: 96.4 % / Redundancy: 7 % / CC1/2: 0.998 / Rpim(I) all: 0.035 / Rsym value: 0.066 / Net I/σ(I): 10.3
Reflection shellResolution: 2.4→2.4962 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1255 / CC1/2: 0.896 / Rpim(I) all: 0.245 / Rsym value: 0.461

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UEP

6uep


Resolution: 2.4→77.615 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1286 10.04 %
Rwork0.2117 11517 -
obs0.2155 12803 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.07 Å2 / Biso mean: 44.3471 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: final / Resolution: 2.4→77.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 565 10 75 2120
Biso mean--80.5 46.04 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032140
X-RAY DIFFRACTIONf_angle_d0.5683003
X-RAY DIFFRACTIONf_chiral_restr0.042341
X-RAY DIFFRACTIONf_plane_restr0.003280
X-RAY DIFFRACTIONf_dihedral_angle_d11.6671198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4001-2.49620.29451450.2399125599
2.4962-2.60980.30541410.2589127898
2.6098-2.74740.27551390.2544127999
2.7474-2.91950.34991440.2769128799
2.9195-3.14490.32871440.2798127798
3.1449-3.46140.26811400.2363129097
3.4614-3.96230.24991380.2185122793
3.9623-4.99190.19541420.1512128794
4.9919-77.6150.19111530.1759133793
Refinement TLS params.Method: refined / Origin x: 5.276 Å / Origin y: 17.0499 Å / Origin z: 22.0968 Å
111213212223313233
T0.2227 Å2-0.0067 Å2-0.0426 Å2-0.2281 Å20.0092 Å2--0.2398 Å2
L0.4785 °20.1477 °20.0166 °2-0.5626 °2-0.1062 °2--0.6344 °2
S-0.0413 Å °0.0145 Å °0.0199 Å °0.0151 Å °-0.0765 Å °-0.0825 Å °-0.0573 Å °0.0156 Å °-0.1341 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB12 - 198
2X-RAY DIFFRACTION1allC201 - 214
3X-RAY DIFFRACTION1allD215 - 228
4X-RAY DIFFRACTION1allI22 - 23
5X-RAY DIFFRACTION1allS1 - 75

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