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- EMDB-16274: RNA polymerase II pre-initiation complex with the distal +1 nucle... -
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Basic information
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Title | RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) | |||||||||
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![]() | Mammalian PIC / +1 nucleosome / transcription initiation / TRANSCRIPTION | |||||||||
Function / homology | ![]() MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / DNA 5'-3' helicase / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / hair follicle maturation ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / DNA 5'-3' helicase / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / 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 / RNA polymerase transcription factor SL1 complex / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II 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 / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase II core complex assembly / 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 / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / G protein-coupled receptor internalization / female germ cell nucleus / male pronucleus / transcription factor TFIIH core complex / female pronucleus / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / Abortive elongation of HIV-1 transcript in the absence of Tat / germinal vesicle / RNA polymerase II general transcription initiation factor binding / [RNA-polymerase]-subunit kinase / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / Signaling by FGFR2 IIIa TM / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / 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 / protein acetylation / : / : / bone mineralization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Abril-Garrido J / Dienemann C / Grabbe F / Velychko T / Lidschreiber M / Wang H / Cramer P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Authors: Julio Abril-Garrido / Christian Dienemann / Frauke Grabbe / Taras Velychko / Michael Lidschreiber / Haibo Wang / Patrick Cramer / ![]() Abstract: At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further ...At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 213.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 76.8 KB 76.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 58.9 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 17.1 KB | ||
Others | ![]() ![]() | 194.7 MB 194.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 840.8 KB | Display | ![]() |
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Full document | ![]() | 840.4 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bvwMC ![]() 8byqC ![]() 8bz1C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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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
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16274_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : RNA polymerase II pre-initiation complex with the distal +1 nucleosome
+Supramolecule #1: RNA polymerase II pre-initiation complex with the distal +1 nucleosome
+Supramolecule #2: General transcription factor IIH
+Supramolecule #3: Mammalian RNA polymerase II
+Supramolecule #4: Nucleosome (protein)
+Supramolecule #5: Nucleosome (DNA)
+Supramolecule #6: General transcription factor IIB
+Supramolecule #7: TATA-box binding protein
+Supramolecule #8: General transcription factor IIF
+Supramolecule #9: General transcription factor IIA
+Supramolecule #10: General transcription factor IIE
+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: Cyclin-dependent kinase 7
+Macromolecule #10: Cyclin-H
+Macromolecule #11: DNA-directed RNA polymerase subunit
+Macromolecule #12: DNA-directed RNA polymerase subunit beta
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #14: RNA polymerase II subunit D
+Macromolecule #15: DNA-directed RNA polymerase II subunit E
+Macromolecule #16: DNA-directed RNA polymerase II subunit F
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #19: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #20: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #21: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #22: RNA polymerase II subunit K
+Macromolecule #23: Transcription initiation factor IIB
+Macromolecule #25: TATA-box-binding protein
+Macromolecule #26: General transcription factor IIF subunit 1
+Macromolecule #27: General transcription factor IIF subunit 2
+Macromolecule #29: Transcription initiation factor IIA subunit 1
+Macromolecule #30: Transcription initiation factor IIA subunit 2
+Macromolecule #31: General transcription factor IIE subunit 1
+Macromolecule #32: Transcription initiation factor IIE subunit beta
+Macromolecule #33: Unassigned peptide, likely XPB
+Macromolecule #34: Unassigned peptide, likely TFIIE-beta
+Macromolecule #35: Histone H3.2
+Macromolecule #36: Histone H4
+Macromolecule #37: Histone H2A type 1
+Macromolecule #38: Histone H2B 1.1
+Macromolecule #24: Non-template DNA
+Macromolecule #28: Template DNA
+Macromolecule #39: IRON/SULFUR CLUSTER
+Macromolecule #40: ZINC ION
+Macromolecule #41: 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: 7.5 |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 41517 / Average exposure time: 3.0 sec. / Average electron dose: 41.58 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-8bvw: |