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- PDB-6uer: Crystal form 2: Structure of TBP bound to C-C mismatch at pH 7 -

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Basic information

Entry
Database: PDB / ID: 6uer
TitleCrystal form 2: Structure of TBP bound to C-C mismatch at pH 7
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
  • TATA-box-binding protein 1
KeywordsDNA BINDING PROTEIN/DNA / TBP / TATA box / transcription / mismatch site / NER / 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: 2.5 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
A: TATA-box-binding protein 1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
B: TATA-box-binding protein 1
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)66,0706
Polymers66,0706
Non-polymers00
Water1629
1
A: TATA-box-binding protein 1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)33,0353
Polymers33,0353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-17 kcal/mol
Surface area13000 Å2
MethodPISA
2
B: TATA-box-binding protein 1
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)33,0353
Polymers33,0353
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-16 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.879, 91.228, 97.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2
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*CP*GP*GP*GP*CP*A)-3')


Mass: 4313.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Mass: 4206.740 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0, 3.4 M sodium formate

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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 6M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→65.708 Å / Num. obs: 63767 / % possible obs: 99.7 % / Redundancy: 4 % / CC1/2: 0.989 / Rpim(I) all: 0.066 / Rsym value: 0.117 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.562 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1816 / CC1/2: 0.945 / Rpim(I) all: 0.416 / Rsym value: 0.654

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UEP

6uep


Resolution: 2.5→65.708 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 2005 7.16 %
Rwork0.1991 26008 -
obs0.2019 63767 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.3 Å2 / Biso mean: 85.8344 Å2 / Biso min: 43.85 Å2
Refinement stepCycle: final / Resolution: 2.5→65.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 1130 0 9 4091
Biso mean---63.61 -
Num. residues----430
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.56250.36791370.33731816100
2.5625-2.63180.35481460.32591829100
2.6318-2.70930.43291350.32981844100
2.7093-2.79670.37191450.33331812100
2.7967-2.89670.38921470.3141845100
2.8967-3.01270.28511340.26831830100
3.0127-3.14980.28621440.25111854100
3.1498-3.31580.23981400.22771839100
3.3158-3.52360.27491460.21261857100
3.5236-3.79560.20981400.18611849100
3.7956-4.17750.22041460.1761861100
4.1775-4.78180.21241420.15041891100
4.7818-6.0240.2081460.16161902100
6.024-65.7080.19321570.18197999
Refinement TLS params.Method: refined / Origin x: 14.9007 Å / Origin y: 23.9915 Å / Origin z: 7.3564 Å
111213212223313233
T0.4729 Å2-0.0226 Å2-0.0072 Å2-0.6111 Å20.0192 Å2--0.5286 Å2
L0.8805 °20.1285 °2-0.3207 °2-2.1339 °2-0.2424 °2--1.5559 °2
S-0.0089 Å °0.0332 Å °0.1521 Å °0.037 Å °0.3001 Å °0.1392 Å °-0.0959 Å °-0.1239 Å °-0.2801 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 198
2X-RAY DIFFRACTION1allC201 - 214
3X-RAY DIFFRACTION1allD215 - 228
4X-RAY DIFFRACTION1allB12 - 198
5X-RAY DIFFRACTION1allE201 - 214
6X-RAY DIFFRACTION1allF215 - 228
7X-RAY DIFFRACTION1allS1 - 9

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