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Yorodumi- EMDB-57390: RNA polymerase II initially transcribing complex with a 2-nt RNA ... -
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Basic information
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| Title | RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome | |||||||||
Map data | filtered based on local resolution | |||||||||
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Keywords | RNA polymerase II / TRANSCRIPTION | |||||||||
| Function / homology | Function and homology informationMMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / transcription factor TFIIE complex / RNA polymerase transcription factor SL1 complex / hair cell differentiation / nucleotide-excision repair factor 3 complex / phosphatase activator activity / nucleotide-excision repair, preincision complex assembly ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / transcription factor TFIIE complex / RNA polymerase transcription factor SL1 complex / hair cell differentiation / nucleotide-excision repair factor 3 complex / phosphatase activator activity / nucleotide-excision repair, preincision complex assembly / TFIIF-class transcription factor complex binding / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / RNA polymerase I core promoter sequence-specific DNA binding / CAK-ERCC2 complex / transcription factor TFIIF complex / 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 / 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 / transcription factor TFIIA complex / 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 - 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 / mRNA Splicing - Major Pathway / mRNA Polyadenylation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA Polymerase III Abortive And Retractive Initiation / male pronucleus / regulation of cyclin-dependent protein serine/threonine kinase activity / female pronucleus / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA polymerase II general transcription initiation factor binding / cyclin-dependent protein serine/threonine kinase activator activity / G protein-coupled receptor internalization / DNA 5'-3' helicase / Abortive elongation of HIV-1 transcript in the absence of Tat / nuclear thyroid hormone receptor binding / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / embryonic organ development / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / Processing of Capped Intron-Containing Pre-mRNA / ATPase activator activity / positive regulation of transcription by RNA polymerase III / mRNA Splicing - Minor Pathway / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / DNA topological change / RNA Polymerase I Transcription Initiation / response to UV / RNA polymerase II transcribes snRNA genes / DNA 3'-5' helicase / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription by RNA polymerase III / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of transcription initiation by RNA polymerase II Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() unidentified adenovirus | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Zhan Y / Abril-Garrido J / Dienemann C / Cramer P | |||||||||
| Funding support | Germany, 1 items
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Citation | Journal: Mol Cell / Year: 2026Title: The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation. Authors: Yumeng Zhan / Julio Abril-Garrido / Frauke Grabbe / Paulina Seweryn / Ute Neef / Christian Dienemann / Patrick Cramer / ![]() Abstract: Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre- ...Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre-initiation complex (PIC) assembly and RNA Pol II pausing, but its function in transcription initiation and the transition to elongation remains unclear. Here, we investigate the transcription initiation-elongation transition in vitro using DNA templates containing a +1 nucleosome and present cryo-electron microscopy (cryo-EM) structures of five intermediate states. First, after PIC assembly, ATP binding to TFIIH enables the +1 nucleosome to evict TFIID from the PIC. Following DNA opening, the +1 nucleosome stimulates TFIIH translocase activity and initial RNA synthesis. Finally, after DNA bubble rewinding, the +1 nucleosome removes TFIIH from the early elongation complex for promoter escape. Our findings show that the +1 nucleosome not only acts passively in PIC assembly and RNA Pol II pausing but rather has active functions during the initiation-elongation transition of transcription. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_57390.map.gz | 240.3 MB | EMDB map data format | |
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| Header (meta data) | emd-57390-v30.xml emd-57390.xml | 68 KB 68 KB | Display Display | EMDB header |
| Images | emd_57390.png | 63 KB | ||
| Filedesc metadata | emd-57390.cif.gz | 16.2 KB | ||
| Others | emd_57390_additional_1.map.gz emd_57390_half_map_1.map.gz emd_57390_half_map_2.map.gz | 336.8 MB 339.1 MB 338 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-57390 ftp://data.pdbj.org/pub/emdb/structures/EMD-57390 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 29vfMC ![]() 29tkC ![]() 29wdC ![]() 30ffC ![]() 30fhC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_57390.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | filtered based on local resolution | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: consensus map
| File | emd_57390_additional_1.map | ||||||||||||
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| Annotation | consensus map | ||||||||||||
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| Density Histograms |
-Half map: half map
| File | emd_57390_half_map_1.map | ||||||||||||
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| Annotation | half map | ||||||||||||
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| Density Histograms |
-Half map: half map
| File | emd_57390_half_map_2.map | ||||||||||||
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| Annotation | half map | ||||||||||||
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Sample components
+Entire : RNA polymerase II elongation complex with the +1 nucleosome
+Supramolecule #1: RNA polymerase II elongation complex with the +1 nucleosome
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #2: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #3: General transcription factor IIH subunit 1
+Macromolecule #4: General transcription factor IIH subunit 4
+Macromolecule #5: General transcription factor IIH subunit 2
+Macromolecule #6: General transcription factor IIH subunit 3
+Macromolecule #7: General transcription factor IIH subunit 5
+Macromolecule #8: CDK-activating kinase assembly factor MAT1
+Macromolecule #9: DNA-directed RNA polymerase subunit
+Macromolecule #10: DNA-directed RNA polymerase subunit beta
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #12: RNA polymerase II subunit D
+Macromolecule #13: DNA-directed RNA polymerase II subunit E
+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-a
+Macromolecule #20: RNA polymerase II subunit K
+Macromolecule #21: Transcription initiation factor IIB
+Macromolecule #23: TATA-box-binding protein
+Macromolecule #25: General transcription factor IIF subunit 1
+Macromolecule #26: General transcription factor IIF subunit 2
+Macromolecule #28: Transcription initiation factor IIA subunit 1
+Macromolecule #29: Transcription initiation factor IIA subunit 2
+Macromolecule #30: General transcription factor IIE subunit 1
+Macromolecule #31: Transcription initiation factor IIE subunit beta
+Macromolecule #32: Histone H3.2
+Macromolecule #33: Histone H4
+Macromolecule #34: Histone H2A type 1
+Macromolecule #35: Histone H2B 1.1
+Macromolecule #22: DNA (213-MER)
+Macromolecule #27: DNA (227-MER)
+Macromolecule #24: RNA (5'-R(P*AP*C)-3')
+Macromolecule #36: IRON/SULFUR CLUSTER
+Macromolecule #37: ZINC ION
+Macromolecule #38: MAGNESIUM ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
unidentified adenovirus
Authors
Germany, 1 items
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Trichoplusia ni (cabbage looper)

Processing
FIELD EMISSION GUN
