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- PDB-8wan: Structure of transcribing complex 4 (TC4), the initially transcri... -
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Basic information
Entry | Database: PDB / ID: 8wan | ||||||
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Title | Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. | ||||||
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![]() | TRANSCRIPTION / transcribing complex / de novo transcription initiation / initially transcribing complex (ITC) | ||||||
Function / homology | ![]() spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex ...spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly / TFIIH-class transcription factor complex binding / nucleotide-excision repair, DNA duplex unwinding / negative regulation of protein autoubiquitination / central nervous system myelin formation / transcription factor TFTC complex / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / negative regulation of MHC class II biosynthetic process / hair follicle maturation / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / SLIK (SAGA-like) complex / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / UV protection / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 I core promoter sequence-specific DNA binding / DNA 5'-3' helicase / hepatocyte differentiation / transcriptional start site selection at RNA polymerase II promoter / 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 / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / transcription factor TFIIF complex / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of response to cytokine stimulus / maintenance of protein location in nucleus / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of androgen receptor activity / transcription factor TFIIA complex / female germ cell nucleus / G protein-coupled receptor internalization / C2H2 zinc finger domain binding / male pronucleus / transcription factor TFIIH core complex / female pronucleus / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / transcription regulator inhibitor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / DNA 3'-5' helicase / nuclear vitamin D receptor binding / RNA polymerase binding / germinal vesicle / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / regulation of fat cell differentiation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.07 Å | ||||||
![]() | Chen, X. / Liu, W. / Wang, Q. / Wang, X. / Ren, Y. / Qu, X. / Li, W. / Xu, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural visualization of transcription initiation in action. Authors: Xizi Chen / Weida Liu / Qianmin Wang / Xinxin Wang / Yulei Ren / Xuechun Qu / Wanjun Li / Yanhui Xu / ![]() Abstract: Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted ...Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2.5 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 37398MC ![]() 8wakC ![]() 8walC ![]() 8waoC ![]() 8wapC ![]() 8waqC ![]() 8warC ![]() 8wasC ![]() 8watC ![]() 8wauC ![]() 8wavC ![]() 8wawC ![]() 8waxC ![]() 8wayC ![]() 8wazC ![]() 8wb0C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Protein , 4 types, 4 molecules 0PUz
+General transcription factor IIH subunit ... , 5 types, 5 molecules 12345
+General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 67
+Transcription initiation factor ... , 17 types, 23 molecules ABDdEeFfGHIiJjLlOQRVckm
+General transcription factor IIF subunit ... , 2 types, 2 molecules ST
+DNA chain , 2 types, 2 molecules XY
+DNA-directed RNA polymerase ... , 9 types, 9 molecules opqrstuwy
+DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules vx
+Protein/peptide / RNA chain , 2 types, 2 molecules NZ
+Non-polymers , 4 types, 20 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/W0F.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/W0F.gif)
+Details
-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
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 6.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5141 / Symmetry type: POINT |