+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8308 | ||||||||||||||||||
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Title | Mediator-RNA Polymerase II Pre-Initiation Complex | ||||||||||||||||||
Map data | Mediator-RNA Polymerase II Pre-Initiation Complex | ||||||||||||||||||
Sample |
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Biological species | yeast (yeast) / Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 21.9 Å | ||||||||||||||||||
Authors | Robinson PJ / Bushnell DA / Kornberg RD | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Cell / Year: 2016 Title: Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Authors: Philip J Robinson / Michael J Trnka / David A Bushnell / Ralph E Davis / Pierre-Jean Mattei / Alma L Burlingame / Roger D Kornberg / Abstract: A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass ...A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8308.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-8308-v30.xml emd-8308.xml | 70.2 KB 70.2 KB | Display Display | EMDB header |
Images | emd_8308.png | 48.6 KB | ||
Masks | emd_8308_msk_1.map | 40.6 MB | Mask map | |
Others | emd_8308_half_map_1.map.gz emd_8308_half_map_2.map.gz | 31.3 MB 31.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8308 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8308 | HTTPS FTP |
-Validation report
Summary document | emd_8308_validation.pdf.gz | 426.9 KB | Display | EMDB validaton report |
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Full document | emd_8308_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | emd_8308_validation.xml.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8308 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8308 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8308.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mediator-RNA Polymerase II Pre-Initiation Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8308_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Mediator-RNA Polymerase II Pre-Initiation Complex half-map odd
File | emd_8308_half_map_1.map | ||||||||||||
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Annotation | Mediator-RNA Polymerase II Pre-Initiation Complex half-map odd | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mediator-RNA Polymerase II Pre-Initiation Complex half-map even
File | emd_8308_half_map_2.map | ||||||||||||
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Annotation | Mediator-RNA Polymerase II Pre-Initiation Complex half-map even | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mediator-RNA Polymerase II Pre-Initiation Complex
+Supramolecule #1: Mediator-RNA Polymerase II Pre-Initiation Complex
+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 RPABC 1
+Macromolecule #6: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
+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 RPABC 4
+Macromolecule #13: TRANSCRIPTION INITIATION FACTOR IIB
+Macromolecule #14: TATA-box-binding protein
+Macromolecule #15: Transcription factor TFIIE subunit TFA1
+Macromolecule #16: Transcription factor TFIIE subunit TFA2
+Macromolecule #17: Transcription initiation factor IIA large subunit
+Macromolecule #18: Transcription initiation factor IIA subunit 2
+Macromolecule #19: Transcription initiation factor IIF subunit alpha
+Macromolecule #20: Transcription initiation factor IIF subunit beta
+Macromolecule #21: Transcription initiation factor IIF subunit gamma
+Macromolecule #22: RNA polymerase II transcription factor B subunit 1
+Macromolecule #23: RNA polymerase II transcription factor B subunit 2
+Macromolecule #24: RNA polymerase II transcription factor B subunit 3
+Macromolecule #25: RNA polymerase II transcription factor B subunit 4
+Macromolecule #26: RNA polymerase II transcription factor B subunit 5
+Macromolecule #27: Serine/threonine-protein kinase KIN28
+Macromolecule #28: Cyclin CCL1
+Macromolecule #29: DNA repair helicase RAD3
+Macromolecule #30: Suppressor of stem-loop protein 1
+Macromolecule #31: DNA repair helicase RAD25
+Macromolecule #32: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #33: Mediator of RNA polymerase II transcription subunit 2
+Macromolecule #34: Mediator of RNA polymerase II transcription subunit 3
+Macromolecule #35: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #36: Mediator of RNA polymerase II transcription subunit 5
+Macromolecule #37: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #38: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #39: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #40: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #41: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #42: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #43: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #44: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #45: Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #46: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #47: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #48: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #49: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #50: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #51: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #52: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #53: 108 bp HIS4 promoter fragment
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: 80 mM potassium acetate, 20 mM Tris, pH 7.5, 2 mM magnesium acetate, 5 mM DTT | |||||||||||||||
Grid | Model: Quantifoil R2/1, R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | For cryo-EM, samples were chemically stabilized by fixation in glycerol gradients with increasing concentrations of glutaraldehyde (0-0.1%). Peak gradient fractions (~0.2 mg/mL) containing glutaraldhyde were quenched upon the addition of 50 mM Tris-HCl (pH 7.5) before flash-freezing and storage under liquid nitrogen. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |