+Open data
-Basic information
Entry | Database: PDB / ID: 6kf3 | |||||||||||||||
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Title | Cryo-EM structure of Thermococcus kodakarensis RNA polymerase | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION / apo-RNA polymerase | |||||||||||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / protein dimerization activity / DNA-templated transcription / nucleotide binding / magnesium ion binding ...DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / protein dimerization activity / DNA-templated transcription / nucleotide binding / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||
Authors | Jun, S.-H. / Hyun, J. / Jeong, H. / Cha, J.S. / Kim, H. / Bartlett, M.S. / Cho, H.-S. / Murakami, K.S. | |||||||||||||||
Funding support | Korea, Republic Of, United States, 4items
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Citation | Journal: Nat Commun / Year: 2020 Title: Direct binding of TFEα opens DNA binding cleft of RNA polymerase. Authors: Sung-Hoon Jun / Jaekyung Hyun / Jeong Seok Cha / Hoyoung Kim / Michael S Bartlett / Hyun-Soo Cho / Katsuhiko S Murakami / Abstract: Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron ...Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs. | |||||||||||||||
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 | 6kf3.cif.gz | 590.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kf3.ent.gz | 473 KB | Display | PDB format |
PDBx/mmJSON format | 6kf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kf3_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6kf3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6kf3_validation.xml.gz | 91.5 KB | Display | |
Data in CIF | 6kf3_validation.cif.gz | 140.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/6kf3 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/6kf3 | HTTPS FTP |
-Related structure data
Related structure data | 9960M 6kf4C 6kf9C 6plnC 6xjfC 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 A
#1: Protein | Mass: 103038.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoA' Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE33, DNA-directed RNA polymerase |
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-DNA-directed RNA polymerase subunit ... , 8 types, 8 molecules BCDHKLNP
#2: Protein | Mass: 127468.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoB Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE32, DNA-directed RNA polymerase |
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#3: Protein | Mass: 43727.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoA'' Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE34, DNA-directed RNA polymerase |
#4: Protein | Mass: 29429.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoD Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JJF4, DNA-directed RNA polymerase |
#7: Protein | Mass: 9522.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoH Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE31, DNA-directed RNA polymerase |
#8: Protein | Mass: 6286.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoK Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JJD0, DNA-directed RNA polymerase |
#9: Protein | Mass: 11013.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoL Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE88, DNA-directed RNA polymerase |
#10: Protein | Mass: 7601.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoN Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JJC9, DNA-directed RNA polymerase |
#11: Protein/peptide | Mass: 5553.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RpoP Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JDM8, DNA-directed RNA polymerase |
-DNA-directed RNA polymerase, subunit ... , 2 types, 2 molecules EF
#5: Protein | Mass: 21893.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: RpoE Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIY4 |
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#6: Protein | Mass: 14519.659 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: RpoF Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0901 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JI52 |
-Non-polymers , 2 types, 6 molecules
#12: Chemical | ChemComp-MG / |
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#13: Chemical | ChemComp-ZN / |
-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 / Type: COMPLEX / Entity ID: #1-#11 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.38 MDa |
Source (natural) | Organism: Thermococcus kodakarensis KOD1 (archaea) |
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) / Strain: BL21 |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 278 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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139242 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT |