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- PDB-1cdw: HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1cdw
TitleHUMAN TBP CORE DOMAIN COMPLEXED WITH DNA
Components
  • DNA (5'-D(*CP*AP*GP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*CP*TP*G)-3')
  • PROTEIN (TATA BINDING PROTEIN (TBP))
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION INITIATION / DNA BINDING / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIA complex / female germ cell nucleus / RNA Polymerase III Abortive And Retractive Initiation / male pronucleus ...RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIA complex / female germ cell nucleus / RNA Polymerase III Abortive And Retractive Initiation / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / RNA Polymerase I Transcription Termination / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / euchromatin / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / enzyme binding / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
TATA-Binding Protein / TATA-Binding Protein / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNikolov, D.B. / Chen, H. / Halay, E.D. / Hoffmann, A. / Roeder, R.G. / Burley, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal structure of a human TATA box-binding protein/TATA element complex.
Authors: Nikolov, D.B. / Chen, H. / Halay, E.D. / Hoffman, A. / Roeder, R.G. / Burley, S.K.
History
DepositionApr 11, 1996Processing site: NDB
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,0223
Polymers30,0223
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.800, 78.000, 97.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: DNA chain DNA (5'-D(*CP*TP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*CP*TP*G)-3')


Mass: 4922.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*GP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*AP*G)-3')


Mass: 4873.178 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TATA BINDING PROTEIN (TBP))


Mass: 20227.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20226
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMhTBPc-DNA1drop
2200 mM1dropKCl
3250 mMammonium acetate1drop
45 mM1dropMgCl2
55 mM1dropCaCl2
610 mMdithiothreitol1drop
710 %(v/v)glycerol1drop
82 %(v/v)ethylene glycol1drop
940 mMTris-HCl1drop
108-12 %(v/v)glycerol1reservoir
1120 mMdithiothreitol1reservoir
1240 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→18 Å / Num. obs: 28256 / % possible obs: 98.6 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.227 / % possible all: 90.3
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 18 Å / % possible obs: 98.6 % / Num. measured all: 214715

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TBP2-DNA COMPLEX

Resolution: 1.9→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.258 -8.7 %
Rwork0.189 --
obs0.189 26476 88.4 %
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 650 0 280 2351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 8.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31 Å2

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