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Yorodumi- PDB-1tbp: CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INT... -
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-Basic information
Entry | Database: PDB / ID: 1tbp | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR INTERACTION WITH DNA | ||||||
Components | TATA-BINDING PROTEIN | ||||||
Keywords | BINDING PROTEIN | ||||||
Function / homology | Function and homology information TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter ...TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA genes / 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 / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / DNA-templated transcription initiation / disordered domain specific binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Chasman, D.I. / Flaherty, K.M. / Sharp, P.A. / Kornberg, R.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Crystal structure of yeast TATA-binding protein and model for interaction with DNA. Authors: Chasman, D.I. / Flaherty, K.M. / Sharp, P.A. / Kornberg, R.D. #1: Journal: Nature / Year: 1992 Title: Crystal Structure of TFIID TATA-Box Binding Protein Authors: Nikolov, D.B. / Hu, S.-H. / Lin, J. / Gasch, A. / Hoffmann, A. / Horikoshi, M. / Chua, N.-H. / 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 | 1tbp.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tbp.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 1tbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tbp_validation.pdf.gz | 368 KB | Display | wwPDB validaton report |
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Full document | 1tbp_full_validation.pdf.gz | 379.2 KB | Display | |
Data in XML | 1tbp_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1tbp_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/1tbp ftp://data.pdbj.org/pub/pdb/validation_reports/tb/1tbp | 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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Atom site foot note | 1: CIS PROLINE - PRO A 109 / 2: CIS PROLINE - PRO A 200 / 3: CIS PROLINE - PRO B 109 / 4: CIS PROLINE - PRO B 200 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.846596, -0.25936, 0.464766), Vector: |
-Components
#1: Protein | Mass: 20164.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P13393 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.25 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
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Refinement | Resolution: 2.6→6 Å / Rfactor Rwork: 0.211 / Rfactor obs: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 6 Å / Rfactor obs: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.64 |