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Open data
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Basic information
Entry | Database: PDB / ID: 7oha | |||||||||
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Title | nucleosome with TBP and TFIIA bound at SHL +2 | |||||||||
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![]() | TRANSCRIPTION / DNA binding protein nucleosome | |||||||||
Function / homology | ![]() transcription factor TFIIA complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity ...transcription factor TFIIA complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Wang, H. / Cramer, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures and implications of TBP-nucleosome complexes. Authors: Haibo Wang / Le Xiong / Patrick Cramer / ![]() Abstract: The TATA box-binding protein (TBP) is highly conserved throughout eukaryotes and plays a central role in the assembly of the transcription preinitiation complex (PIC) at gene promoters. TBP binds and ...The TATA box-binding protein (TBP) is highly conserved throughout eukaryotes and plays a central role in the assembly of the transcription preinitiation complex (PIC) at gene promoters. TBP binds and bends DNA, and directs adjacent binding of the transcription factors TFIIA and TFIIB for PIC assembly. Here, we show that yeast TBP can bind to a nucleosome containing the Widom-601 sequence and that TBP-nucleosome binding is stabilized by TFIIA. We determine three cryo-electron microscopy (cryo-EM) structures of TBP-nucleosome complexes, two of them containing also TFIIA. TBP can bind to superhelical location (SHL) -6, which contains a TATA-like sequence, but also to SHL +2, which is GC-rich. Whereas binding to SHL -6 can occur in the absence of TFIIA, binding to SHL +2 is only observed in the presence of TFIIA and goes along with detachment of upstream terminal DNA from the histone octamer. TBP-nucleosome complexes are sterically incompatible with PIC assembly, explaining why a promoter nucleosome generally impairs transcription and must be moved before initiation can occur. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.1 KB | Display | ![]() |
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PDB format | ![]() | 255.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 869 KB | Display | ![]() |
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Full document | ![]() | 879.8 KB | Display | |
Data in XML | ![]() | 41.4 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12898MC ![]() 7oh9C ![]() 7ohbC ![]() 7ohcC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 5 types, 9 molecules AEBFCGDHK
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #7: Protein | | Mass: 27042.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SPT15 / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44520.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#6: DNA chain | Mass: 44991.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
-Transcription initiation factor IIA ... , 2 types, 2 molecules LM
#8: Protein | Mass: 19432.029 Da / Num. of mol.: 1 / Mutation: residues 95-209 are deleted Source method: isolated from a genetically manipulated source Details: Toa1 protein with residues 95-209 deleted. Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS5691, SCNYR20_0002031500, SCP684_0003030900 Production host: ![]() ![]() |
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#9: Protein | Mass: 13473.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS3356, PACBIOSEQ_LOCUS3547, PACBIOSEQ_LOCUS3591, PACBIOSEQ_LOCUS3602, PACBIOSEQ_LOCUS3607, PACBIOSEQ_LOCUS3639, PACBIOSEQ_LOCUS3680, PACBIOSEQ_LOCUS3892, PACBIOSEQ_LOCUS3963 Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Nucleosome with TBP / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.23 MDa / Experimental value: YES |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 41.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130350 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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