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Yorodumi- PDB-8cro: Cryo-EM structure of Pyrococcus furiosus transcription elongation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cro | ||||||
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Title | Cryo-EM structure of Pyrococcus furiosus transcription elongation complex | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA / Polymerase / Elongation / Complex / Pyrococcus furiosus / Archaea / DNA | ||||||
Function / homology | Function and homology information RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I 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 / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Tarau, D.M. / Grunberger, F. / Reichelt, R. / Heiss, F.B. / Pilsl, M. / Hausner, W. / Engel, C. / Grohmann, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2024 Title: Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment. Authors: Daniela Tarău / Felix Grünberger / Michael Pilsl / Robert Reichelt / Florian Heiß / Sabine König / Henning Urlaub / Winfried Hausner / Christoph Engel / Dina Grohmann / Abstract: Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, ...Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cro.cif.gz | 611.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cro.ent.gz | 479.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cro_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8cro_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8cro_validation.xml.gz | 93 KB | Display | |
Data in CIF | 8cro_validation.cif.gz | 141.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/8cro ftp://data.pdbj.org/pub/pdb/validation_reports/cr/8cro | HTTPS FTP |
-Related structure data
Related structure data | 16809MC 8okiC 8orqC 8p2iC 8rboC 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 ... , 11 types, 11 molecules ABCDEFLHNKP
#1: Protein | Mass: 103612.250 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpoA1, rpo1N, PFDSM3638_07875 / Production host: Pyrococcus furiosus DSM 3638 (archaea) References: UniProt: A0A5C0XPL7, DNA-directed RNA polymerase |
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#2: Protein | Mass: 127188.898 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: PF1564 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0M3 |
#3: Protein | Mass: 44468.156 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo1C, rpoA2, PF1562 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0M5, DNA-directed RNA polymerase |
#4: Protein | Mass: 29817.182 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo3, rpoD, PF1647 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0E4, DNA-directed RNA polymerase |
#5: Protein | Mass: 21731.455 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo7 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U439 |
#6: Protein | Mass: 14116.311 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo4, rpoF, PF1036 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U216, DNA-directed RNA polymerase |
#7: Protein | Mass: 11132.764 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo11, rpoL, PF0050 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U4N1, DNA-directed RNA polymerase |
#8: Protein | Mass: 9260.792 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo5, rpoH, PF1565 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0M2, DNA-directed RNA polymerase |
#9: Protein | Mass: 7800.158 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo10, rpoN, PF1643 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: P60292, DNA-directed RNA polymerase |
#10: Protein | Mass: 6243.490 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo6, rpoK, PF1642 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0E8, DNA-directed RNA polymerase |
#11: Protein/peptide | Mass: 5770.050 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: rpo12, rpoP, PF2009 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8TZI3, DNA-directed RNA polymerase |
-DNA chain , 2 types, 2 molecules XY
#12: DNA chain | Mass: 6190.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus DSM 3638 (archaea) |
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#13: DNA chain | Mass: 2963.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus DSM 3638 (archaea) |
-RNA chain , 1 types, 1 molecules Z
#14: RNA chain | Mass: 2909.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus DSM 3638 (archaea) |
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-Non-polymers , 2 types, 6 molecules
#15: Chemical | ChemComp-ZN / #16: Chemical | ChemComp-MG / | |
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-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
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 88.73 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333535 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | Accession code: 6kf9 / Source name: SwissModel / Type: in silico model | ||||||||||||||||||||||||||||
Refine LS restraints |
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