+Open data
-Basic information
Entry | Database: PDB / ID: 8gzh | ||||||
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Title | Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA/RNA / Cryo-EM / Synechocystis sp. PCC 6803 / Syn6803 / Transcription initiation / CTP-bound RPitc / Transcription / Cyanobacteria / TRANSCRIPTION-DNA-RNA complex | ||||||
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 | Synechocystis sp. PCC 6803 (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å | ||||||
Authors | You, L.L. / Shen, L.Q. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc Authors: You, L.L. / Shen, L.Q. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gzh.cif.gz | 856.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gzh.ent.gz | 651.8 KB | Display | PDB format |
PDBx/mmJSON format | 8gzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gzh_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8gzh_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8gzh_validation.xml.gz | 98.5 KB | Display | |
Data in CIF | 8gzh_validation.cif.gz | 158.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/8gzh ftp://data.pdbj.org/pub/pdb/validation_reports/gz/8gzh | HTTPS FTP |
-Related structure data
Related structure data | 34398MC 8gzgC 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 ... , 5 types, 6 molecules ABCDEZ
#1: Protein | Mass: 36657.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: rpoA, sll1818 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73297, DNA-directed RNA polymerase #2: Protein | | Mass: 123719.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: rpoB, sll1787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P77965, DNA-directed RNA polymerase #3: Protein | | Mass: 71072.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: rpoC1, slr1265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74177, DNA-directed RNA polymerase #4: Protein | | Mass: 8749.776 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: rpoZ, ssl2982 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74352, DNA-directed RNA polymerase #6: Protein | | Mass: 145371.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: rpoC2, sll1789 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73334, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules 12
#7: DNA chain | Mass: 20810.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#8: DNA chain | Mass: 20673.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain , 2 types, 2 molecules F3
#5: Protein | Mass: 50335.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: sigA, rpoD, rpoD1, slr0653 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74565 |
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#9: RNA chain | Mass: 1239.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 5 molecules
#10: Chemical | #11: Chemical | #12: Chemical | ChemComp-CTP / | |
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-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: The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc Type: COMPLEX / Entity ID: #1-#9 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Value: 0.5 MDa / Experimental value: YES | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 295 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 defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2297 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 681334 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145731 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |