+Open data
-Basic information
Entry | Database: PDB / ID: 6gym | |||||||||
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Title | Structure of a yeast closed complex with distorted DNA (CCdist) | |||||||||
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Keywords | TRANSCRIPTION / rna polymerase ii / transcription initiation / promoter opening | |||||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / 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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / 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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / DNA 5'-3' helicase / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA binding, bending / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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-templated transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / ATPase activator activity / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Dienemann, C. / Schwalb, B. / Schilbach, S. / Cramer, P. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Mol Cell / Year: 2019 Title: Promoter Distortion and Opening in the RNA Polymerase II Cleft. Authors: Christian Dienemann / Björn Schwalb / Sandra Schilbach / Patrick Cramer / Abstract: Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron ...Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening. | |||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 6gym.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gym.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6gym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gym_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6gym_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6gym_validation.xml.gz | 198.4 KB | Display | |
Data in CIF | 6gym_validation.cif.gz | 313.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/6gym ftp://data.pdbj.org/pub/pdb/validation_reports/gy/6gym | HTTPS FTP |
-Related structure data
Related structure data | 0092MC 0090C 0091C 6gykC 6gylC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
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