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- PDB-6ueo: Structure of A. thaliana TBP-AC mismatch DNA site -

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Basic information

Entry
Database: PDB / ID: 6ueo
TitleStructure of A. thaliana TBP-AC mismatch DNA site
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*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 / mismatch base pair / NER / DNA binding protein / TATA box / 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 Å
AuthorsSchumacher, M.A.
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
B: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
C: DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
D: TATA-box-binding protein 1
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*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')
G: TATA-box-binding protein 1
H: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
I: DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
J: TATA-box-binding protein 1
K: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
L: 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)132,23712
Polymers132,23712
Non-polymers00
Water8,737485
1
A: TATA-box-binding protein 1
B: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
C: 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)33,0593
Polymers33,0593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-12 kcal/mol
Surface area13000 Å2
MethodPISA
2
D: TATA-box-binding protein 1
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*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)33,0593
Polymers33,0593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-15 kcal/mol
Surface area12990 Å2
MethodPISA
3
G: TATA-box-binding protein 1
H: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
I: 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)33,0593
Polymers33,0593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-14 kcal/mol
Surface area12940 Å2
MethodPISA
4
J: TATA-box-binding protein 1
K: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
L: 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)33,0593
Polymers33,0593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-14 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.242, 55.512, 146.340
Angle α, β, γ (deg.)89.970, 90.030, 90.140
Int Tables number1
Space group name H-MP1

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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.: 4
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*GP*GP*GP*CP*A)-3')


Mass: 4337.855 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium acetate, 38% ethylene glycol

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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: Aug 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→73.1 Å / Num. obs: 77170 / % possible obs: 90.7 % / Redundancy: 1.7 % / Biso Wilson estimate: 33.29 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.057 / Rsym value: 0.058 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4480 / CC1/2: 0.0965 / Rpim(I) all: 0.196 / Rsym value: 0.198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QNE

1qne


Resolution: 2→55.512 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.91
RfactorNum. reflection% reflection
Rfree0.2498 1993 2.58 %
Rwork0.2138 --
obs0.2147 77107 85.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.41 Å2 / Biso mean: 39.4452 Å2 / Biso min: 15.42 Å2
Refinement stepCycle: final / Resolution: 2→55.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 2268 0 489 8661
Biso mean---43.39 -
Num. residues----860
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.27791250.272448072
2.05-2.10550.29341400.2595539786
2.1055-2.16740.30921410.2553535986
2.1674-2.23740.28911470.2504534885
2.2374-2.31740.33531380.258521684
2.3174-2.41010.2961430.2526530485
2.4101-2.51980.25761500.2399552988
2.5198-2.65270.21731440.2286552688
2.6527-2.81890.30891360.2327536886
2.8189-3.03650.23711450.2337537886
3.0365-3.3420.22831440.2221552989
3.342-3.82550.25761500.2026546287
3.8255-4.81940.23241560.1803565691
4.8194-55.5120.20951340.1841556289
Refinement TLS params.Method: refined / Origin x: 10.1308 Å / Origin y: -17.0656 Å / Origin z: -25.3459 Å
111213212223313233
T0.1688 Å2-0.0033 Å2-0.0034 Å2-0.183 Å20.0027 Å2--0.1967 Å2
L0.023 °20.0053 °2-0.0227 °2-0.04 °20.043 °2--0.3283 °2
S0.0405 Å °-0.0068 Å °0.0021 Å °-0.0039 Å °0.0057 Å °0.0244 Å °-0.0026 Å °-0.0027 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 198
2X-RAY DIFFRACTION1allB201 - 214
3X-RAY DIFFRACTION1allC215 - 228
4X-RAY DIFFRACTION1allD12 - 198
5X-RAY DIFFRACTION1allE201 - 214
6X-RAY DIFFRACTION1allF215 - 228
7X-RAY DIFFRACTION1allG12 - 198
8X-RAY DIFFRACTION1allH201 - 214
9X-RAY DIFFRACTION1allI215 - 228
10X-RAY DIFFRACTION1allJ12 - 198
11X-RAY DIFFRACTION1allK201 - 214
12X-RAY DIFFRACTION1allL215 - 228
13X-RAY DIFFRACTION1allS1 - 489

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