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Open data
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Basic information
Entry | Database: PDB / ID: 1nh2 | ||||||
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Title | Crystal structure of a yeast TFIIA/TBP/DNA complex | ||||||
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![]() | TRANSCRIPTION/DNA / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase III / 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 / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase III / 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 / RNA Polymerase II Pre-transcription Events / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription factor TFIID complex / 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 / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / disordered domain specific binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bleichenbacher, M. / Tan, S. / Richmond, T.J. | ||||||
![]() | ![]() Title: Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. Authors: Bleichenbacher, M. / Tan, S. / Richmond, T.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.8 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.5 KB | Display | ![]() |
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Full document | ![]() | 483 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules EF
#1: DNA chain | Mass: 5143.980 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4871.202 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Transcription initiation factor ... , 4 types, 4 molecules ABCD
#3: Protein | Mass: 20120.754 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 180 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SPT15 OR BTF1 OR YER148W / Production host: ![]() ![]() |
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#4: Protein | Mass: 6135.750 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 54 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TOA1 OR YOR194C / Production host: ![]() ![]() |
#5: Protein | Mass: 8915.654 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 77 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TOA1 OR YOR194C / Production host: ![]() ![]() |
#6: Protein | Mass: 13341.874 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TOA2 OR YKL058W / Production host: ![]() ![]() |
-Non-polymers , 1 types, 477 molecules ![](data/chem/img/HOH.gif)
#7: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 217906 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.3 Å2 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 48353 / % possible obs: 94.9 % / Redundancy: 4.5 % / Num. measured all: 217906 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / % possible obs: 98.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.147 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 76.6007 Å2 / ksol: 0.460095 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.23 Å / Luzzati sigma a free: 0.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.236 / Rfactor Rwork: 0.205 |