[English] 日本語
Yorodumi- PDB-8cro: Cryo-EM structure of Pyrococcus furiosus transcription elongation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cro | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Pyrococcus furiosus transcription elongation complex | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / RNA / Polymerase / Elongation / Complex / Pyrococcus furiosus / Archaea / DNA | ||||||
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 / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding ...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
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment Authors: Tarau, D.M. / Grunberger, F. / Pilsl, M. / Reichelt, R. / Heiss, F.B. / Koenig, S. / Urlaub, H. / Hausner, W. / Engel, C. / Grohmann, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8cro.cif.gz | 610.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
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
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.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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 |
---|---|
#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) |
---|---|
#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) |
---|
-Non-polymers , 2 types, 6 molecules
#15: Chemical | ChemComp-ZN / #16: Chemical | ChemComp-MG / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||
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 |
---|---|
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 | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
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 |
|