+Open data
-Basic information
Entry | Database: PDB / ID: 1cdw | ||||||
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Title | HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/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 / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / 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 / 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 / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / male germ cell nucleus / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / SIRT1 negatively regulates rRNA expression / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / euchromatin / DNA-binding transcription factor binding / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / Estrogen-dependent gene expression / transcription cis-regulatory region binding / transcription by RNA polymerase II / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nikolov, D.B. / Chen, H. / Halay, E.D. / Hoffmann, A. / Roeder, R.G. / Burley, S.K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cdw.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cdw.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cdw_validation.pdf.gz | 378.4 KB | Display | wwPDB validaton report |
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Full document | 1cdw_full_validation.pdf.gz | 383.6 KB | Display | |
Data in XML | 1cdw_validation.xml.gz | 6 KB | Display | |
Data in CIF | 1cdw_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/1cdw ftp://data.pdbj.org/pub/pdb/validation_reports/cd/1cdw | 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: 4922.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4873.178 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→18 Å / Num. obs: 28256 / % possible obs: 98.6 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TBP2-DNA COMPLEX Resolution: 1.9→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 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: 1.9 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 8.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31 Å2 |