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- EMDB-33031: 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 initial complex with two Zur dimers. | |||||||||
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Function / homology | ![]() negative regulation of siderophore biosynthetic process / regulation of secondary metabolite biosynthetic process / bacterial-type RNA polymerase holo enzyme binding / DNA-binding transcription repressor activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
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Method | ![]() ![]() | |||||||||
![]() | Yang X / Zheng J | |||||||||
Funding support | 1 items
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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
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Downloads & links
-EMDB archive
Map data | ![]() | 6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.3 KB 27.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 18.7 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Others | ![]() ![]() | 200.2 MB 200.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7x74MC ![]() 7vo0C ![]() 7vo9C ![]() 7vpdC ![]() 7vpzC ![]() 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: 1.1 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 transcription initia...
+Supramolecule #1: Cryo-EM structure of Streptomyces coelicolor transcription initia...
+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 #6: Putative metal uptake regulation protein
+Macromolecule #7: DNA (84-MER)
+Macromolecule #8: DNA (84-MER)
+Macromolecule #9: RNA
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
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Aggregation state | particle |
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Sample preparation
Concentration | 0.8 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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |