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Yorodumi- PDB-5fz5: Transcription initiation complex structures elucidate DNA opening (CC) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fz5 | ||||||
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Title | Transcription initiation complex structures elucidate DNA opening (CC) | ||||||
Components |
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Keywords | TRANSCRIPTION / GENE EXPRESSION / TRANSCRIPTION INITIATION | ||||||
Function / homology | Function and homology information RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding ...RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / 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 / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / : / RNA polymerase I preinitiation complex assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / DNA binding, bending / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA polymerase II general transcription initiation factor activity / 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 / transcription factor TFIID complex / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / protein phosphatase activator activity / tRNA transcription by RNA polymerase III / 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 elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / translesion synthesis / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / disordered domain specific binding / single-stranded DNA binding / ribosome biogenesis / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / nucleotide binding / mRNA binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) SYNTHETIC (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å | ||||||
Authors | Plaschka, C. / Hantsche, M. / Dienemann, C. / Burzinski, C. / Plitzko, J. / Cramer, P. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Transcription initiation complex structures elucidate DNA opening. Authors: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer / Abstract: Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) ...Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AM" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AM" 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 "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 | 5fz5.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fz5.ent.gz | 871 KB | Display | PDB format |
PDBx/mmJSON format | 5fz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/5fz5 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/5fz5 | HTTPS FTP |
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-Related structure data
Related structure data | 3383MC 3375C 3376C 3377C 3378C 3379C 3380C 3381C 3382C 5fywC 5ip7C 5ip9C C: citing same article (ref.) M: map data used to model this data |
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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 II SUBUNIT ... , 7 types, 7 molecules ABCDGIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P04050, DNA-directed RNA polymerase |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P08518, DNA-directed RNA polymerase |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P16370 |
#4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20433 |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P34087 |
#9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P27999 |
#11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P38902 |
-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: BJ5464 RPB3 HIS-BIO / 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: BJ5464 RPB3 HIS-BIO / 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: BJ5464 RPB3 HIS-BIO / 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: BJ5464 RPB3 HIS-BIO / 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: BJ5464 RPB3 HIS-BIO / References: UniProt: P40422 |
-Protein , 2 types, 2 molecules MO
#13: Protein | Mass: 38257.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29055 |
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#15: Protein | Mass: 27042.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13393 |
-SYNTHETIC CLOSED PROMOTER DNA ... , 2 types, 2 molecules NT
#14: DNA chain | Mass: 17254.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NON-TEMPLATE STRAND / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
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#18: DNA chain | Mass: 26172.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE STRAND / Source: (synth.) SYNTHETIC (others) |
-TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ... , 2 types, 2 molecules QR
#16: Protein | Mass: 82320.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41895 |
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#17: Protein | Mass: 46684.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PETDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41896, DNA helicase |
-TRANSCRIPTION INITIATION FACTOR IIA ... , 2 types, 2 molecules UV
#19: Protein | Mass: 32230.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: BJ5464 RPB3 HIS-BIO / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P32773 |
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#20: Protein | Mass: 13473.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P32774 |
-TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ... , 2 types, 2 molecules WX
#21: Protein | Mass: 54804.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36100 |
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#22: Protein | Mass: 37050.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36145 |
-Non-polymers , 2 types, 11 molecules
#23: Chemical | ChemComp-ZN / #24: Chemical | ChemComp-MG / | |
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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: YEAST POL II TRANSCRIPTION INITIATION COMPLEX (CLOSED DNA) Type: COMPLEX |
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Buffer solution | Name: 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT pH: 7.5 Details: 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT |
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 IV / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jun 20, 2016 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 X / Calibrated magnification: 37037 X / Nominal defocus max: 5000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Num. digital images: 959 |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: RELION 1.3 / Resolution: 8.8 Å / Num. of particles: 5690 Details: THE MODEL FOR THE CLOSED COMPLEX WAS DERIVED FROM THE OPEN COMPLEX MODEL (5FYW). THREE RIGID-BODY GROUPS (1. POL II, TFIIA, TFIIB, TBP, TFIIE E-RIBBON AND TFIIF DIMERIZATION DOMAIN, 2. TFIIE ...Details: THE MODEL FOR THE CLOSED COMPLEX WAS DERIVED FROM THE OPEN COMPLEX MODEL (5FYW). THREE RIGID-BODY GROUPS (1. POL II, TFIIA, TFIIB, TBP, TFIIE E-RIBBON AND TFIIF DIMERIZATION DOMAIN, 2. TFIIE DOMAINS TFA1 AND TFA2 WH, 3.TFIIE TFA2 WH1 AND TFIIF TFG2 WH) WERE INDIVIDUALLY FITTED INTO THE CLOSED COMPLEX EM DENSITY BY AN AUTOMATED CORRELATION SEARCH IN SITUS. TO MODEL CLOSED PROMOTER DNA, UPSTREAM DNA WAS EXTENDED WITH CANONICAL DUPLEX B-FORM DNA IN COOT AND RIGID-BODY FITTED IN UCSF CHIMERA TO REFLECT THE DENSITY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3383. (DEPOSITION ID: 14367). Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 8.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.8 Å
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