+Open data
-Basic information
Entry | Database: PDB / ID: 1tgh | ||||||
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Title | TATA BINDING PROTEIN (TBP)/DNA COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / DNA BINDING PROTEIN / DNA / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / 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 / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus ...RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / 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 / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / RNA Polymerase I Transcription Termination / 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 / RNA Polymerase I Transcription Initiation / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / TFIIB-class transcription factor binding / RNA polymerase II general transcription initiation factor activity / 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 / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Juo, Z.S. / Dickerson, R.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: How proteins recognize the TATA box. Authors: Juo, Z.S. / Chiu, T.K. / Leiberman, P.M. / Baikalov, I. / Berk, A.J. / Dickerson, R.E. #1: Journal: Nat.Struct.Biol. / Year: 1994 Title: 1.9 A Resolution Refined Structure of TBP Recognizing the Minor Groove of TATAAAAG Authors: Kim, J.L. / Burley, S.K. #2: Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tgh.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tgh.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tgh_validation.pdf.gz | 425.1 KB | Display | wwPDB validaton report |
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Full document | 1tgh_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 1tgh_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1tgh_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/1tgh ftp://data.pdbj.org/pub/pdb/validation_reports/tg/1tgh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | | Mass: 20801.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TBP / Plasmid: PET21D / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P20226 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 92 K |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 19, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. obs: 9013 |
-Processing
Software |
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Refinement | Resolution: 2.9→8 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Rfactor obs: 0.2145 / Rfactor Rfree: 0.2946 / Rfactor Rwork: 0.2145 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.141 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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