+Open data
-Basic information
Entry | Database: PDB / ID: 8jke | ||||||
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Title | AfsR(T337A) transcription activation complex | ||||||
Components |
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Keywords | GENE REGULATION/DNA / RNA polymerase / SARP regulator / gene regulation / TRANSCRIPTION / GENE REGULATION-DNA complex | ||||||
Function / homology | Function and homology information pigment binding / bacterial-type RNA polymerase holo enzyme binding / phosphorelay signal transduction system / sigma factor activity / rRNA transcription / 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 / phosphorelay signal transduction system / sigma factor activity / rRNA transcription / 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 | Streptomyces coelicolor A3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å | ||||||
Authors | Wang, Y. / Zheng, J. | ||||||
Funding support | China, 1items
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Citation | Journal: PLoS Biol / Year: 2024 Title: Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces. Authors: Yiqun Wang / Xu Yang / Feng Yu / Zixin Deng / Shuangjun Lin / Jianting Zheng / Abstract: Streptomyces antibiotic regulatory proteins (SARPs) are widely distributed activators of antibiotic biosynthesis. Streptomyces coelicolor AfsR is an SARP regulator with an additional nucleotide- ...Streptomyces antibiotic regulatory proteins (SARPs) are widely distributed activators of antibiotic biosynthesis. Streptomyces coelicolor AfsR is an SARP regulator with an additional nucleotide-binding oligomerization domain (NOD) and a tetratricopeptide repeat (TPR) domain. Here, we present cryo-electron microscopy (cryo-EM) structures and in vitro assays to demonstrate how the SARP domain activates transcription and how it is modulated by NOD and TPR domains. The structures of transcription initiation complexes (TICs) show that the SARP domain forms a side-by-side dimer to simultaneously engage the afs box overlapping the -35 element and the σHrdB region 4 (R4), resembling a sigma adaptation mechanism. The SARP extensively interacts with the subunits of the RNA polymerase (RNAP) core enzyme including the β-flap tip helix (FTH), the β' zinc-binding domain (ZBD), and the highly flexible C-terminal domain of the α subunit (αCTD). Transcription assays of full-length AfsR and truncated proteins reveal the inhibitory effect of NOD and TPR on SARP transcription activation, which can be eliminated by ATP binding. In vitro phosphorylation hardly affects transcription activation of AfsR, but counteracts the disinhibition of ATP binding. Overall, our results present a detailed molecular view of how AfsR serves to activate transcription. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jke.cif.gz | 799.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jke.ent.gz | 619.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jke_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8jke_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8jke_validation.xml.gz | 114.4 KB | Display | |
Data in CIF | 8jke_validation.cif.gz | 179.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/8jke ftp://data.pdbj.org/pub/pdb/validation_reports/jk/8jke | HTTPS FTP |
-Related structure data
Related structure data | 36370MC 8hvrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 6 molecules ABKCDE
#1: Protein | Mass: 36734.641 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: rpoA, GTW64_13255 / Production host: Escherichia coli BL21(DE3) (bacteria) 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.) Streptomyces coelicolor A3(2) (bacteria) Gene: rpoB, SCO4654, SCD82.26 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L0L0, DNA-directed RNA polymerase #3: Protein | | Mass: 145912.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: rpoC, SCO4655, SCD40A.01, SCD82.27 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8CJT1, DNA-directed RNA polymerase #4: Protein | | Mass: 9716.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: rpoZ, SCO1478, SC9C5.02c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KXS1, DNA-directed RNA polymerase |
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-Protein , 4 types, 5 molecules FGHIJ
#5: Protein | Mass: 58188.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: hrdB, sigA, SCO5820, SC5B8.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18183 |
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#6: Protein | Mass: 14146.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: rbpA, SCO1421 / Production host: Escherichia coli BL21(DE3) (bacteria) |
#7: Protein | Mass: 17855.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: SCD8A.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L0Q9 |
#8: Protein | Mass: 107983.930 Da / Num. of mol.: 2 / Mutation: T337A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: afsR, afsB, SCO4426, SCD6.04c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25941 |
-DNA chain , 2 types, 2 molecules OP
#9: DNA chain | Mass: 19863.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria) |
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#10: DNA chain | Mass: 20086.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria) |
-Non-polymers , 2 types, 3 molecules
#11: Chemical | ChemComp-MG / |
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#12: Chemical |
-Details
Has ligand of interest | N |
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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 |
-Sample preparation
Component | Name: AfsR(T337A)-dependent transcription activation complex with afsS promoter Type: COMPLEX / Entity ID: #1-#10 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.7 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Streptomyces coelicolor A3(2) (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||||||||||||
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 | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum |
Image scans | Movie frames/image: 32 |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 193644 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45208 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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