+Open data
-Basic information
Entry | Database: PDB / ID: 5fmf | ||||||
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Title | the P-lobe of RNA polymerase II pre-initiation complex | ||||||
Components |
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Keywords | TRANSCRIPTION / PRE-INITIATION COMPLEX / RNA POLYMERASE / TFIIE / TFIIH / TFIIB / TBP / TFIIF / PROTEIN | ||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / regulation of mRNA 3'-end processing / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / regulation of mRNA 3'-end processing / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / DNA 5'-3' helicase / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / transcription preinitiation complex / DNA binding, bending / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / poly(A)+ mRNA export from nucleus / 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 / 3'-5' DNA helicase activity / TP53 Regulates Transcription of DNA Repair Genes / transcription factor TFIID complex / termination of RNA polymerase II transcription / 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 polymerase II general transcription initiation factor activity / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / RNA Polymerase I Promoter Escape / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / ATPase activator activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Estrogen-dependent gene expression / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly / transcription-coupled nucleotide-excision repair / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / positive regulation of translational initiation / translesion synthesis / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / isomerase activity / transcription antitermination / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription elongation by RNA polymerase II / transcription coregulator activity / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å | ||||||
Authors | Murakami, K. / Tsai, K. / Kalisman, N. / Bushnell, D.A. / Asturias, F.J. / Kornberg, R.D. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Structure of an RNA polymerase II preinitiation complex. Authors: Kenji Murakami / Kuang-Lei Tsai / Nir Kalisman / David A Bushnell / Francisco J Asturias / Roger D Kornberg / Abstract: The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the ...The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BQ" 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 "GE" 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 "MA" 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 "UA" 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 | 5fmf.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fmf.ent.gz | 971.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fmf_validation.pdf.gz | 1021.3 KB | Display | wwPDB validaton report |
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Full document | 5fmf_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5fmf_validation.xml.gz | 248.7 KB | Display | |
Data in CIF | 5fmf_validation.cif.gz | 359.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fmf ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fmf | HTTPS FTP |
-Related structure data
Related structure data | 3114MC 3115C 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 REPAIR HELICASE ... , 2 types, 2 molecules 1Y
#1: Protein | Mass: 56309.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q00578, DNA helicase |
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#27: Protein | Mass: 89899.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P06839, DNA helicase |
-Protein , 2 types, 2 molecules 2Q
#2: Protein | Mass: 19687.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P07273 |
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#19: Protein | Mass: 20120.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P13393 |
-DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 6 types, 6 molecules ABCGIK
#3: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase |
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#4: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase |
#5: Protein | Mass: 29921.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16370 |
#9: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P34087 |
#11: Protein | Mass: 13942.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P27999 |
#13: Protein | Mass: 13113.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38902 |
-RNA POLYMERASE II PRE-INITIATION COMPLEX, ... , 3 types, 3 molecules DMU
#6: Protein | Mass: 20433.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20433*PLUS |
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#15: Protein | Mass: 13588.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32773*PLUS |
#23: Protein | Mass: 17708.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P41895*PLUS |
-DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ... , 5 types, 5 molecules EFHJL
#7: Protein | Mass: 24985.895 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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#8: Protein | Mass: 9675.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20435 |
#10: 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 |
#12: Protein | Mass: 7647.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22139 |
#14: Protein/peptide | Mass: 5252.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40422 |
-DNA chain , 2 types, 2 molecules NT
#16: DNA chain | Mass: 22483.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
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#22: DNA chain | Mass: 21908.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
-TRANSCRIPTION INITIATION FACTOR ... , 5 types, 5 molecules OPRSV
#17: Protein | Mass: 13473.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32774 |
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#18: Protein | Mass: 38257.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P29055 |
#20: Protein | Mass: 18612.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P36100 |
#21: Protein | Mass: 14524.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P36145 |
#24: Protein | Mass: 20710.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P41896, DNA helicase |
-RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT ... , 2 types, 2 molecules WX
#25: Protein | Mass: 7338.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q02939 |
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#26: Protein | Mass: 7139.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q3E7C1 |
-Non-polymers , 2 types, 11 molecules
#28: Chemical | #29: 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: REFINED P-LOBE OF YEAST RNA POLYMERASE II PRE-INITIATION COMPLEX Type: COMPLEX |
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Buffer solution | Name: 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC pH: 7.6 Details: 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC |
Specimen | Conc.: 0.3 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- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III, |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Nov 14, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 22500 X / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
-Processing
EM software | Name: SPARX / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: SPARX | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 6 Å / Num. of particles: 7578 / Actual pixel size: 1.315 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3114. (DEPOSITION ID: 13659). Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6 Å
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