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- PDB-7x75: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7x75 | ||||||
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Title | Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers | ||||||
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![]() | GENE REGULATION / rna polymerase / zinc uptake regulator | ||||||
Function / homology | ![]() regulation of secondary metabolite biosynthetic process / negative regulation of siderophore biosynthetic process / bacterial-type RNA polymerase holo enzyme binding / 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 ...regulation of secondary metabolite biosynthetic process / negative regulation of siderophore biosynthetic process / bacterial-type RNA polymerase holo enzyme binding / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 796 KB | Display | ![]() |
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PDB format | ![]() | 630.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 109.9 KB | Display | |
Data in CIF | ![]() | 175.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33032MC ![]() 7vo0C ![]() 7vo9C ![]() 7vpdC ![]() 7vpzC ![]() 7x74C ![]() 7x76C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 6 molecules ABSCDE
#1: Protein | Mass: 36734.641 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rpoA, GTW64_13255 / Production host: ![]() ![]() References: UniProt: A0A6G2M9E1, DNA-directed RNA polymerase #2: Protein | | Mass: 128644.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-471 / A3(2) / M145 / Gene: rpoB, SCO4654, SCD82.26 / Production host: ![]() ![]() #3: Protein | | Mass: 145912.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-471 / A3(2) / M145 / Gene: rpoC, SCO4655, SCD40A.01, SCD82.27 / Production host: ![]() ![]() #4: Protein | | Mass: 9716.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-471 / A3(2) / M145 / Gene: rpoZ, SCO1478, SC9C5.02c / Production host: ![]() ![]() |
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-Protein , 2 types, 7 molecules FGHKLMN
#5: Protein | Mass: 58188.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-471 / A3(2) / M145 / Gene: hrdB, sigA, SCO5820, SC5B8.10 / Production host: ![]() ![]() |
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#6: Protein | Mass: 16904.840 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO2508 / Production host: ![]() ![]() |
-DNA chain , 2 types, 2 molecules OP
#7: DNA chain | Mass: 25808.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#8: DNA chain | Mass: 26017.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 2 types, 21 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#9: Chemical | ChemComp-MG / |
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#10: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.56 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30218 / Symmetry type: POINT |