+Open data
-Basic information
Entry | Database: PDB / ID: 5fj9 | ||||||
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Title | Cryo-EM structure of yeast apo RNA polymerase III at 4.6 A | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA POLYMERASE III / POL III / RNA POLYMERASE | ||||||
Function / homology | Function and homology information RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / nucleotidyltransferase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / peroxisome / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Hoffmann, N.A. / Jakobi, A.J. / Moreno-Morcillo, M. / Glatt, S. / Kosinski, J. / Hagen, W.J. / Sachse, C. / Muller, C.W. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Molecular structures of unbound and transcribing RNA polymerase III. Authors: Niklas A Hoffmann / Arjen J Jakobi / María Moreno-Morcillo / Sebastian Glatt / Jan Kosinski / Wim J H Hagen / Carsten Sachse / Christoph W Müller / Abstract: Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet ...Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. Here we present the cryo-electron microscopy structures of the Saccharomyces cerevisiae Pol III elongating complex at 3.9 Å resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 Å resolution, respectively, which allow the building of a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82-C34-C31 heterotrimer in close proximity to the stalk. The C53-C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets. | ||||||
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 | 5fj9.cif.gz | 983.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fj9.ent.gz | 800.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fj9_validation.pdf.gz | 893.6 KB | Display | wwPDB validaton report |
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Full document | 5fj9_full_validation.pdf.gz | 979.7 KB | Display | |
Data in XML | 5fj9_validation.xml.gz | 136.4 KB | Display | |
Data in CIF | 5fj9_validation.cif.gz | 203.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fj9 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fj9 | HTTPS FTP |
-Related structure data
Related structure data | 3179MC 3178C 3180C 5fj8C 5fjaC 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
-DNA-DIRECTED RNA POLYMERASE III SUBUNIT ... , 10 types, 10 molecules ABDGIMNOPQ
#1: Protein | Mass: 162517.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04051, DNA-directed RNA polymerase |
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#2: Protein | Mass: 129629.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22276, DNA-directed RNA polymerase |
#4: Protein | Mass: 18623.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P47076 |
#7: Protein | Mass: 24349.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P35718 |
#9: Protein | Mass: 12525.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q04307 |
#13: Protein | Mass: 32178.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P36121 |
#14: Protein | Mass: 46751.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P25441 |
#15: Protein | Mass: 74112.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32349 |
#16: Protein | Mass: 36174.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32910 |
#17: Protein | Mass: 10348.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P17890 |
-DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ... , 2 types, 2 molecules CK
#3: Protein | Mass: 37732.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P07703 |
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#11: Protein | Mass: 16167.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P28000 |
-DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20434 |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20435 |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20436 |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22139 |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40422 |
-Non-polymers , 1 types, 6 molecules
#18: Chemical | ChemComp-ZN / |
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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: S.CEREVISIAE APO RNA POLYMERASE III (CLOSED CLAMP CONFORMATION) Type: COMPLEX |
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Buffer solution | Name: 150MM (NH4)2SO4, 15MM TRIS, 10MM DTT / pH: 7.5 / Details: 150MM (NH4)2SO4, 15MM TRIS, 10MM DTT |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK III, METHOD- 2.5 UL OF SAMPLE WAS APPLIED 15 SECONDS WAIT TIME BLOT FOR 9 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Dec 15, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 4200 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 4.6 Å / Num. of particles: 68818 / Nominal pixel size: 1.084 Å / Actual pixel size: 1.084 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA DATA FROM EMDB EMD-3179. (DEPOSITION ID: 13849). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: REAL-SPACE CORRELATION / Details: METHOD--LOCAL CORRELATION | ||||||||||||
Refinement | Highest resolution: 4.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.6 Å
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