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- EMDB-36914: Cryo-EM structure of Streptomyces coelicolor transcription initia... -
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Open data
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Basic information
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Title | Cryo-EM structure of Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR | |||||||||
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![]() | transcription factor / TRANSCRIPTION-DNA complex / GENE REGULATION | |||||||||
Function / homology | ![]() pigment binding / bacterial-type RNA polymerase holo enzyme binding / nucleoid / sigma factor activity / phosphorelay signal transduction system / antibiotic biosynthetic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / ADP binding ...pigment binding / bacterial-type RNA polymerase holo enzyme binding / nucleoid / sigma factor activity / phosphorelay signal transduction system / antibiotic biosynthetic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / ADP binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Lin W / Shi J / Xu JC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into transcription activation of the antibiotic regulatory protein, AfsR. Authors: Jing Shi / Zonghang Ye / Zhenzhen Feng / Aijia Wen / Lu Wang / Zhipeng Zhang / Liqiao Xu / Qian Song / Fulin Wang / Tianyu Liu / Shuang Wang / Yu Feng / Wei Lin / ![]() Abstract: The antibiotic regulatory proteins (SARPs) are ubiquitously distributed transcription activators in and control antibiotics biosynthesis and morphological differentiation. However, the molecular ...The antibiotic regulatory proteins (SARPs) are ubiquitously distributed transcription activators in and control antibiotics biosynthesis and morphological differentiation. However, the molecular mechanism behind SARP-dependent transcription initiation remains elusive. We here solve the cryo-EM structure of an AfsR-loading RNA polymerase (RNAP)-promoter intermediate complex (AfsR-RPi) including the RNAP, a large SARP member AfsR, and its target promoter DNA that retains the upstream portion straight. The structure reveals that one dimeric N-terminal AfsR-SARP domain (AfsR-SARP) specifically engages with the same face of the AfsR-binding sites by the conserved DNA-binding domains (DBDs), replacing σR4 to bind the suboptimal -35 element, and shortens the spacer between the -10 and -35 elements. Notably, the AfsR-SARPs also recruit RNAP through extensively interacting with its conserved domains (β flap, σR4, and αCTD). Thus, these macromolecular snapshots support a general model and provide valuable clues for SARP-dependent transcription activation in . | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.1 KB 26.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10 KB | Display | ![]() |
Images | ![]() | 53.1 KB | ||
Filedesc metadata | ![]() | 8.8 KB | ||
Others | ![]() ![]() | 65.4 MB 65.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k60MC 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: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
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Density Histograms |
-Half map: #2
File | emd_36914_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Streptomyces coelicolor transcription initiation complex with the...
+Supramolecule #1: Streptomyces coelicolor transcription initiation complex with the...
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: RNA polymerase principal sigma factor HrdB
+Macromolecule #8: Regulatory protein AfsR
+Macromolecule #6: Non-template strand DNA for AfsS promoter
+Macromolecule #7: Template strand DNA for AfsS promoter
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC 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: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |