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Yorodumi- PDB-8re4: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8re4 | ||||||
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Title | Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex | ||||||
Components |
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Keywords | TRANSCRIPTION / initiation / rna polymerase / sigma54 | ||||||
Function / homology | Function and homology information RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription antitermination / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Klebsiella oxytoca (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Gao, F. / Zhang, X. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Structural basis of σ displacement and promoter escape in bacterial transcription. Authors: Forson Gao / Fuzhou Ye / Bowen Zhang / Nora Cronin / Martin Buck / Xiaodong Zhang / Abstract: Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma ...Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma (σ) factors. σ recruits RNAP to the promoter DNA region, located upstream of the transcription start site (TSS) and facilitates open complex formation, where double-stranded DNA is opened up into a transcription bubble and template strand DNA is positioned inside RNAP for initial RNA synthesis. During initial transcription, RNAP remains bound to σ and upstream DNA, presumably with an enlarging transcription bubble. The release of RNAP from upstream DNA is required for promoter escape and processive transcription elongation. Bacteria sigma factors can be broadly separated into two classes with the majority belonging to the σ class, represented by the σ that regulates housekeeping genes. σ forms a class on its own and regulates stress response genes. Extensive studies on σ have revealed the molecular mechanisms of the σ dependent process while how σ transitions from initial transcription to elongation is currently unknown. Here, we present a series of cryo-electron microscopy structures of the RNAP-σ initial transcribing complexes with progressively longer RNA, which reveal structural changes that lead to promoter escape. Our data show that initially, the transcription bubble enlarges, DNA strands scrunch, reducing the interactions between σ and DNA strands in the transcription bubble. RNA extension and further DNA scrunching help to release RNAP from σ and upstream DNA, enabling the transition to elongation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8re4.cif.gz | 756.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8re4.ent.gz | 584.8 KB | Display | PDB format |
PDBx/mmJSON format | 8re4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8re4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8re4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8re4_validation.xml.gz | 102.8 KB | Display | |
Data in CIF | 8re4_validation.cif.gz | 158.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/8re4 ftp://data.pdbj.org/pub/pdb/validation_reports/re/8re4 | HTTPS FTP |
-Related structure data
Related structure data | 19079MC 8reaC 8rebC 8recC 8redC 8reeC 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, 5 molecules ABCDE
#1: Protein | Mass: 35726.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residues missing between Chain A and B due to missing densities Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase #2: Protein | | Mass: 150691.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpoB / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A8V2 #3: Protein | | Mass: 152040.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpoC / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A8T7 #4: Protein | | Mass: 8449.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A800, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules NT
#6: DNA chain | Mass: 14429.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Klebsiella oxytoca (bacteria) |
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#8: DNA chain | Mass: 15461.913 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Klebsiella oxytoca (bacteria) |
-Protein / RNA chain , 2 types, 2 molecules MR
#5: Protein | Mass: 42687.988 Da / Num. of mol.: 1 / Mutation: R336A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Klebsiella oxytoca (bacteria) |
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#7: RNA chain | Mass: 1561.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GCCGC / Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Klebsiella oxytoca (bacteria) |
-Non-polymers , 2 types, 3 molecules
#9: Chemical | ChemComp-MG / |
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#10: 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: RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Source (recombinant) | Organism: Escherichia coli K-12 (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 570815 / Symmetry type: POINT | ||||||||||||||||||||||||
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