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Yorodumi- PDB-6n4c: EM structure of the DNA wrapping in bacterial open transcription ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n4c | ||||||
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Title | EM structure of the DNA wrapping in bacterial open transcription initiation complex | ||||||
Components |
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Keywords | transcription/dna / DNA wrapping / bacterial transcription initiation complex / transmission electron microscopy / single particle analysis. / TRANSCRIPTION / transcription-dna complex | ||||||
Function / homology | Function and homology information sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / 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 / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Enterobacteria phage lambda (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 17 Å | ||||||
Authors | Florez-Ariza, A. / Cassago, A. / de Oliveira, P.S.L. / Guerra, D.G. / Portugal, R.V. | ||||||
Citation | Journal: Biorxiv / Year: 2020 Title: Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation Authors: Sosa, R. / Florez-Ariza, A. / Diaz-Celis, C. / Onoa, B. / Cassago, A. / de Oliveira, P.S.L. / Portugal, R.V. / Guerra, D.G. / Bustamante, C. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6n4c.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6n4c.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6n4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n4c_validation.pdf.gz | 779 KB | Display | wwPDB validaton report |
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Full document | 6n4c_full_validation.pdf.gz | 876.9 KB | Display | |
Data in XML | 6n4c_validation.xml.gz | 99.7 KB | Display | |
Data in CIF | 6n4c_validation.cif.gz | 163 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/6n4c ftp://data.pdbj.org/pub/pdb/validation_reports/n4/6n4c | HTTPS FTP |
-Related structure data
Related structure data | 0340MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules F
#1: Protein | Mass: 64322.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P00579 |
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-DNA-directed RNA polymerase subunit ... , 5 types, 5 molecules CDABE
#2: Protein | Mass: 150689.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 References: UniProt: A0A0A0GWV9, UniProt: P0A8V2*PLUS, DNA-directed RNA polymerase |
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#3: Protein | Mass: 150320.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 References: UniProt: A0A369F490, UniProt: P0A8T7*PLUS, DNA-directed RNA polymerase |
#4: Protein | Mass: 35275.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7Z4, DNA-directed RNA polymerase |
#5: Protein | Mass: 34400.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7Z4, DNA-directed RNA polymerase |
#6: Protein | Mass: 10118.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A800, DNA-directed RNA polymerase |
-DNA chain , 2 types, 2 molecules ab
#7: DNA chain | Mass: 29094.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NT strand DNA (94-MER) / Source: (synth.) Enterobacteria phage lambda (virus) |
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#8: DNA chain | Mass: 28890.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T strand DNA (94-MER) / Source: (synth.) Enterobacteria phage lambda (virus) |
-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: E. coli RNAP-DNA wrapped open complex / Type: COMPLEX Details: Wrapped transcription initiation open complex assembled between E. coli RNAP-sigma 70 holoenzyme and lambda PR wild-type promoter (+18 to -76) Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.50 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli BL21 (bacteria) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE Details: Negatively stained EM specimens were prepared using a 2% uranyl acetate solution. Material: Uranyl Acetate |
Specimen support | Details: na |
-Electron microscopy imaging
Microscopy | Model: JEOL 2100 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||
Particle selection | Num. of particles selected: 60393 | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 17 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Num. of particles: 16015 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: OTHER Details: Initial fiting was done using manual fitting in Chimera. Yasara software was used for energy minimizaton of the DNA and RNAP coordinates model. | |||||||||||||||||||||
Atomic model building | PDB-ID: 4YLN |