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- PDB-1vtl: CO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF A TAT... -

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Basic information

Entry
Database: PDB / ID: 1vtl
TitleCO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF A TATA ELEMENT
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*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
  • TATA BINDING PROTEIN (TBP)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


RNA polymerase II general transcription initiation factor activity / DNA-templated transcription initiation / DNA binding / nucleus
Similarity search - Function
TATA-Binding Protein / 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
DNA / DNA (> 10) / TATA-box-binding protein 1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsKim, J.L. / Nikolov, D.B. / Burley, S.K.
CitationJournal: Nature / Year: 1993
Title: Co-Crystal Structure of TBP Recognizing the Minor Groove of a TATA Element
Authors: Kim, J.L. / Nikolov, D.B. / Burley, S.K.
History
DepositionDec 17, 1993Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
B: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
E: TATA BINDING PROTEIN (TBP)
F: TATA BINDING PROTEIN (TBP)


Theoretical massNumber of molelcules
Total (without water)58,9496
Polymers58,9496
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
B: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
E: TATA BINDING PROTEIN (TBP)


Theoretical massNumber of molelcules
Total (without water)29,4743
Polymers29,4743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
F: TATA BINDING PROTEIN (TBP)


Theoretical massNumber of molelcules
Total (without water)29,4743
Polymers29,4743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.800, 146.500, 57.600
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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.: 2 / Source method: obtained synthetically
#2: 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.: 2 / Source method: obtained synthetically
#3: Protein TATA BINDING PROTEIN (TBP)


Mass: 20914.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / Species: THALIANA / References: UniProt: P28147

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.2 / Details: pH 6.20, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12 WATER1311
25 DTT1614
38 GLYCEROL1917
411 MES112110
514 KCL115113
617 NH4 ACETATE118116
720 WATER121219
823 DTT124222
926 GLYCEROL127225
1029 MES130228

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11231
21231
Diffraction source
SourceID
ROTATING ANODE1
ROTATING ANODE2
Detector
TypeIDDetector
RIGAKU RAXIS IIC1IMAGE PLATE
SIEMENS-NICOLET2AREA DETECTOR
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionHighest resolution: 2.6 Å / Num. all: 47659 / Num. obs: 18312

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.25→6 Å / σ(F): 1.5 /
RfactorNum. reflection
Rwork0.202 -
obs0.202 27613
Refinement stepCycle: LAST / Resolution: 2.25→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 1136 0 0 4057

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