+Open data
-Basic information
Entry | Database: PDB / ID: 7ye1 | |||||||||
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Title | The cryo-EM structure of C. crescentus GcrA-TACup | |||||||||
Components |
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Keywords | TRANSCRIPTION / transcription activator | |||||||||
Function / homology | Function and homology information sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Caulobacter vibrioides NA1000 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Wu, X.X. / Zhang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Cryo-EM structures of Caulobacter crescentus transcription activation complex with an essential cell cycle regulator GcrA Authors: Wu, X.X. / Zhang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ye1.cif.gz | 686.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ye1.ent.gz | 544.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ye1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/7ye1 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/7ye1 | HTTPS FTP |
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-Related structure data
Related structure data | 33761MC 7ye2C 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: 37315.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Strain: NA1000 / Gene: rpoA / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: B8H4F8, DNA-directed RNA polymerase #2: Protein | | Mass: 151085.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Strain: NA1000 / Gene: rpoB / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: B8GZW7, DNA-directed RNA polymerase #3: Protein | | Mass: 154467.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Strain: NA1000 / Gene: rpoC / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: A0A0H3C4W8, DNA-directed RNA polymerase #4: Protein | | Mass: 13289.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Strain: NA1000 / Gene: rpoZ / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: B8H618, DNA-directed RNA polymerase |
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-Protein , 2 types, 2 molecules FG
#5: Protein | Mass: 72770.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Strain: NA1000 / Gene: rpoD / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A0H3CAV3 |
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#6: Protein | Mass: 18515.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides NA1000 (bacteria) Strain: NA1000 / Gene: gcrA / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A0H3C9J4 |
-DNA (57-MER)- ... , 2 types, 2 molecules HI
#7: DNA chain | Mass: 17675.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides NA1000 (bacteria) |
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#8: DNA chain | Mass: 17652.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caulobacter vibrioides NA1000 (bacteria) |
-Non-polymers , 2 types, 4 molecules
#9: Chemical | ChemComp-MG / |
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#10: Chemical |
-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 |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Caulobacter vibrioides NA1000 (bacteria) | ||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli DH5[alpha] (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Cryogen name: NITROGEN |
-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 FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 62.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 287227 / Symmetry type: POINT |