+Open data
-Basic information
Entry | Database: PDB / ID: 5g5l | ||||||
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Title | RNA polymerase I-Rrn3 complex at 4.8 A resolution | ||||||
Components |
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Keywords | RNA POLYMERASE / TRANSCIPTION | ||||||
Function / homology | Function and homology information RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I preinitiation complex assembly / 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 ...RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I preinitiation complex assembly / 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 / regulation of cell size / 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 / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / ribosome biogenesis / peroxisome / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
Authors | Engel, C. / Plitzko, J. / Cramer, P. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: RNA polymerase I-Rrn3 complex at 4.8 Å resolution. Authors: Christoph Engel / Jürgen Plitzko / Patrick Cramer / Abstract: Transcription of ribosomal DNA by RNA polymerase I (Pol I) requires the initiation factor Rrn3. Here we report the cryo-EM structure of the Pol I-Rrn3 complex at 4.8 Å resolution. The structure ...Transcription of ribosomal DNA by RNA polymerase I (Pol I) requires the initiation factor Rrn3. Here we report the cryo-EM structure of the Pol I-Rrn3 complex at 4.8 Å resolution. The structure reveals how Rrn3 binding converts an inactive Pol I dimer into an initiation-competent monomeric complex and provides insights into the mechanisms of Pol I-specific initiation and regulation. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BN" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -4-STRANDED BARREL THIS IS REPRESENTED BY A -3-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5g5l.cif.gz | 834.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g5l.ent.gz | 657.8 KB | Display | PDB format |
PDBx/mmJSON format | 5g5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g5l_validation.pdf.gz | 1016.2 KB | Display | wwPDB validaton report |
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Full document | 5g5l_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5g5l_validation.xml.gz | 148.9 KB | Display | |
Data in CIF | 5g5l_validation.cif.gz | 216.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5l ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5l | HTTPS FTP |
-Related structure data
Related structure data | 3439MC 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 I SUBUNIT ... , 7 types, 7 molecules ABDGIMN
#1: Protein | Mass: 186676.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C-TERMINAL FLAG-10XHIS TAG / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: CB010 / References: UniProt: P10964, DNA-directed RNA polymerase |
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#2: Protein | Mass: 135910.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: CB010 / References: UniProt: P22138, DNA-directed RNA polymerase |
#4: Protein | Mass: 14599.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: CB010 / References: UniProt: P50106 |
#7: Protein | Mass: 36264.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: CB010 / References: UniProt: P46669 |
#9: Protein | Mass: 13676.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: CB010 / References: UniProt: P32529 |
#13: Protein | Mass: 46721.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: CB010 / References: UniProt: Q01080 |
#14: Protein | Mass: 26933.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: CB010 / References: UniProt: P47006 |
-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) / Strain: CB010 / 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) / Strain: CB010 / 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) / Strain: CB010 / 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) / Strain: CB010 / 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) / Strain: CB010 / 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) / Strain: CB010 / 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) / Strain: CB010 / References: UniProt: P40422 |
-Protein / Non-polymers , 2 types, 8 molecules O
#15: Protein | Mass: 72458.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: CB010 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P36070 |
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#16: Chemical | ChemComp-ZN / |
-Details
Sequence details | C-TERMINAL FLAG-10XHIS TAG |
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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 RNA POLYMERASE I BOUND TO THE INITIATION FACTOR RRN3 Type: COMPLEX |
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Buffer solution | Name: 150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT pH: 7.8 Details: 150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE Details: VITROBOT MARK IV, METHOD- 4.5 MICROLITERS OF SAMPLE WAS APPLIED TO GLOW- DISCHARGED QUANTIFOIL R 2- 1 HOLEY CARBON GRIDS, WHICH WERE THEN BLOTTED FOR 8.5S AND PLUNGE- FROZEN IN LIQUID ETHANE. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Mar 27, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 37000 X / Calibrated magnification: 37037 X / Nominal defocus max: 3600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Num. digital images: 1174 |
-Processing
EM software |
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CTF correction | Details: RELION | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: RELION / Resolution: 4.8 Å / Num. of particles: 63445 / Nominal pixel size: 1.35 Å / Actual pixel size: 1.35 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3439. (DEPOSITION ID: 14566). Symmetry type: POINT | ||||||||||||
Atomic model building | B value: 150 / Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building | PDB-ID: 4C2M | ||||||||||||
Refinement | Highest resolution: 4.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.8 Å
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