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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0092 | |||||||||
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Title | Structure of a yeast closed complex with distorted DNA (CCdist) | |||||||||
![]() | Locally filtered map | |||||||||
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![]() | rna polymerase ii / transcription initiation / promoter opening / TRANSCRIPTION | |||||||||
Function / homology | ![]() regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / 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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / RNA polymerase I general transcription initiation factor binding ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / 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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA 3'-5' helicase / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / DNA duplex unwinding / RNA Polymerase I Transcription Initiation / DNA binding, bending / 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 / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / 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 / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / ATPase activator activity / transcription by RNA polymerase III / acetyltransferase activity / transcription factor TFIID complex / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / P-body / ribonucleoside binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
![]() | Dienemann C / Schwalb B | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 110.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 68.2 KB 68.2 KB | Display Display | ![]() |
Images | ![]() | 157.1 KB | ||
Filedesc metadata | ![]() | 14.9 KB | ||
Others | ![]() ![]() | 128.9 MB 129.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 385.9 KB | Display | ![]() |
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Full document | ![]() | 385.1 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gymMC ![]() 0090C ![]() 0091C ![]() 6gykC ![]() 6gylC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Locally filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 1
File | emd_0092_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_0092_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : complex
+Supramolecule #1: complex
+Supramolecule #2: transcription factors
+Supramolecule #3: Polymerase
+Supramolecule #4: Nucleic acid
+Supramolecule #5: transcription factors
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit ...
+Macromolecule #2: General transcription and DNA repair factor IIH subunit TFB1,Gene...
+Macromolecule #3: General transcription and DNA repair factor IIH subunit TFB2,Gene...
+Macromolecule #4: RNA polymerase II transcription factor B subunit 3
+Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4,Gene...
+Macromolecule #6: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #7: General transcription and DNA repair factor IIH subunit SSL1,Gene...
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit ...
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #10: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #12: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #13: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #14: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #19: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #20: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #21: Transcription initiation factor IIB
+Macromolecule #22: TATA-box-binding protein
+Macromolecule #23: Transcription initiation factor IIF subunit alpha
+Macromolecule #24: Transcription initiation factor IIF subunit beta
+Macromolecule #25: Transcription initiation factor IIA large subunit,Transcription i...
+Macromolecule #26: Transcription initiation factor IIA subunit 2
+Macromolecule #27: Transcription initiation factor IIE subunit alpha,Transcription i...
+Macromolecule #28: Transcription initiation factor IIE subunit beta
+Macromolecule #29: Unknown protein
+Macromolecule #30: non-template DNA (HIS4)
+Macromolecule #31: Template DNA (HIS4)
+Macromolecule #32: IRON/SULFUR CLUSTER
+Macromolecule #33: ZINC ION
+Macromolecule #34: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |