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- EMDB-3850: STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFII... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3850 | |||||||||||||||
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Title | STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR | |||||||||||||||
![]() | Transcription initiation complex including Pol II, TBP, the transcription factors TFIIA, -B, -E, -F and -H and core Mediator | |||||||||||||||
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Function / homology | ![]() meiotic gene conversion / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Schilbach S / Hantsche M / Tegunov D / Dienemann C / Wigge C / Urlaub H / Cramer P | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of transcription pre-initiation complex with TFIIH and Mediator. Authors: S Schilbach / M Hantsche / D Tegunov / C Dienemann / C Wigge / H Urlaub / P Cramer / ![]() Abstract: For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron ...For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II. | |||||||||||||||
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 | ![]() | 149.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 89.6 KB 89.6 KB | Display Display | ![]() |
Images | ![]() | 193.9 KB | ||
Filedesc metadata | ![]() | 19.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oqmMC ![]() 3846C ![]() 5oqjC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Transcription initiation complex including Pol II, TBP, the transcription factors TFIIA, -B, -E, -F and -H and core Mediator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
+Entire : Pre-Initiation Complex with core Mediator (PIC-cMed)
+Supramolecule #1: Pre-Initiation Complex with core Mediator (PIC-cMed)
+Supramolecule #2: DNA-directed RNA polymerase
+Supramolecule #3: RNA polymerase II transcription factor B
+Supramolecule #4: Mediator of RNA polymerase II transcription
+Supramolecule #5: DNA
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: Transcription initiation factor IIB
+Macromolecule #15: TATA-box-binding protein
+Macromolecule #16: Transcription initiation factor IIF subunit alpha
+Macromolecule #17: Transcription initiation factor IIF subunit beta
+Macromolecule #19: Transcription initiation factor IIA large subunit
+Macromolecule #20: Transcription initiation factor IIA subunit 2
+Macromolecule #21: Transcription factor TFIIE subunit
+Macromolecule #22: Transcription initiation factor IIE subunit beta
+Macromolecule #23: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #24: General transcription and DNA repair factor IIH subunit TFB1
+Macromolecule #25: General transcription and DNA repair factor IIH subunit TFB2
+Macromolecule #26: RNA polymerase II transcription factor B subunit 3
+Macromolecule #27: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #28: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #29: General transcription and DNA repair factor IIH subunit SSL1
+Macromolecule #30: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #31: Unknown protein
+Macromolecule #32: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #33: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #34: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #35: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #36: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #37: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #38: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #39: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #40: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #41: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #42: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #43: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #44: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #45: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #46: Mediator of RNA polymerase II transcription subunit 31,Mediator o...
+Macromolecule #14: NONTEMPLATE DNA
+Macromolecule #18: TEMPLATE DNA
+Macromolecule #47: ZINC ION
+Macromolecule #48: MAGNESIUM ION
+Macromolecule #49: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.70 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE Details: QUANTIFOIL HOLEY GOLD GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF SAMPLE. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV Details: Grids were blotted for 8 s and plunge-frozen in liquid ethane.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 13000 / Average exposure time: 10.0 sec. / Average electron dose: 42.0 e/Å2 |
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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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.4) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.4) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16000 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-5oqm: |