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- EMDB-34475: Cryo-EM structure of the full transcription activation complex Nt... -
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Open data
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Basic information
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Title | Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC | |||||||||||||||
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![]() | transcription activation complex / coordinated regulation / TRANSCRIPTION | |||||||||||||||
Function / homology | ![]() sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / magnesium ion binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||
![]() | Han SJ / Jiang YL / You LL / Shen LQ / Wu XX / Yang F / Kong WW / Chen ZP / Zhang Y / Zhou CZ | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: DNA looping mediates cooperative transcription activation. Authors: Shu-Jing Han / Yong-Liang Jiang / Lin-Lin You / Li-Qiang Shen / Xiaoxian Wu / Feng Yang / Ning Cui / Wen-Wen Kong / Hui Sun / Ke Zhou / Hui-Chao Meng / Zhi-Peng Chen / Yuxing Chen / Yu Zhang / Cong-Zhao Zhou / ![]() Abstract: Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here ...Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.7 KB 32.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 71 KB | ||
Filedesc metadata | ![]() | 9.9 KB | ||
Others | ![]() ![]() | 151.9 MB 151.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h3vMC ![]() 8h3zC ![]() 8h40C M: atomic model generated by this map C: citing same article ( |
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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: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34475_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34475_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : full transcription activation complex with two activators NtcA an...
+Supramolecule #1: full transcription activation complex with two activators NtcA an...
+Macromolecule #1: DNA (125-MER)
+Macromolecule #2: DNA (125-MER)
+Macromolecule #3: DNA-directed RNA polymerase subunit beta
+Macromolecule #4: DNA-directed RNA polymerase subunit beta'
+Macromolecule #5: DNA-directed RNA polymerase subunit alpha
+Macromolecule #6: DNA-directed RNA polymerase subunit gamma
+Macromolecule #7: DNA-directed RNA polymerase subunit omega
+Macromolecule #8: RNA polymerase sigma factor SigA
+Macromolecule #9: NtcB
+Macromolecule #10: NtcA
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 17 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: 10 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2 and 2 mM DTT | |||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I | |||||||||||||||
Details | This sample was |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5047 / Average electron dose: 50.0 e/Å2 Details: Images were collected in movie-mode at 40 frames per second. |
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: 2.2 µm / Nominal defocus min: 1.2 µm |
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 | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8h3v: |