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- EMDB-32063: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open c... -
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Open data
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Basic information
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Title | Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with one Zur dimers | |||||||||
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![]() | DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() regulation of secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / protein-DNA complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity ...regulation of secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / protein-DNA complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.77 Å | |||||||||
![]() | Yang X / Zheng J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of Streptomyces transcription activation by zinc uptake regulator. Authors: Xu Yang / Yiqun Wang / Guiyang Liu / Zixin Deng / Shuangjun Lin / Jianting Zheng / ![]() Abstract: Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both ...Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both processes by controlling zinc homeostasis. It activates transcription by binding to palindromic Zur-box sequences upstream of -35 elements. Here we deciphered the molecular mechanism by which ScZur interacts with promoter DNA and Sc RNA polymerase (RNAP) by cryo-EM structures and biochemical assays. The ScZur-DNA structures reveal a sequential and cooperative binding of three ScZur dimers surrounding a Zur-box spaced 8 nt upstream from a -35 element. The ScRNAPσHrdB-Zur-DNA structures define protein-protein and protein-DNA interactions involved in the principal housekeeping σHrdB-dependent transcription initiation from a noncanonical promoter with a -10 element lacking the critical adenine residue at position -11 and a TTGCCC -35 element deviating from the canonical TTGACA motif. ScZur interacts with the C-terminal domain of ScRNAP α subunit (αCTD) in a complex structure trapped in an active conformation. Key ScZur-αCTD interfacial residues accounting for ScZur-dependent transcription activation were confirmed by mutational studies. Together, our structural and biochemical results provide a comprehensive model for transcription activation of Zur family regulators. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.9 KB 26.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 100.8 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 8.4 KB | ||
Others | ![]() ![]() | 200.5 MB 200.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vpdMC ![]() 7vo0C ![]() 7vo9C ![]() 7vpzC ![]() 7x74C ![]() 7x75C ![]() 7x76C 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: 1.05 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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-Half map: #2
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-Half map: #1
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Sample components
+Entire : Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open c...
+Supramolecule #1: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open c...
+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 sigma factor SigA
+Macromolecule #6: Putative metal uptake regulation protein
+Macromolecule #7: DNA (84-MER)
+Macromolecule #8: DNA (84-MER)
+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
Concentration | 1.0 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 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 |