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Yorodumi- PDB-8wan: Structure of transcribing complex 4 (TC4), the initially transcri... -
+Open data
-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. | ||||||
Components |
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Keywords | TRANSCRIPTION / transcribing complex / de novo transcription initiation / initially transcribing complex (ITC) | ||||||
Function / homology | Function and homology information spermine transport / negative regulation of MHC class I biosynthetic process / 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 / TFIIH-class transcription factor complex binding / pre-snoRNP complex ...spermine transport / negative regulation of MHC class I biosynthetic process / 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 / TFIIH-class transcription factor complex binding / pre-snoRNP complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / negative regulation of protein autoubiquitination / 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 / hair cell differentiation / negative regulation of MHC class II biosynthetic process / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / RNA polymerase transcription factor SL1 complex / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / SLIK (SAGA-like) complex / UV protection / CAK-ERCC2 complex / transcription factor TFIIK complex / nuclear DNA-directed RNA polymerase complex / RNA polymerase III general transcription initiation factor activity / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus / 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 III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 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 / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / 5'-3' DNA helicase activity / positive regulation of androgen receptor activity / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / nuclear lumen / transcription factor TFIIA complex / G protein-coupled receptor internalization / female germ cell nucleus / C2H2 zinc finger domain binding / box C/D snoRNP assembly / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / SAGA complex / nuclear vitamin D receptor binding / transcription regulator inhibitor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA polymerase binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Amanita phalloides (death cap) Sus scrofa (pig) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.07 Å | ||||||
Authors | Chen, X. / Liu, W. / Wang, Q. / Wang, X. / Ren, Y. / Qu, X. / Li, W. / Xu, Y. | ||||||
Funding support | 1items
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Citation | Journal: Science / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wan.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wan.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8wan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/8wan ftp://data.pdbj.org/pub/pdb/validation_reports/wa/8wan | 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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-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 |