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- PDB-5fz5: Transcription initiation complex structures elucidate DNA opening (CC) -
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Basic information
Entry | Database: PDB / ID: 5fz5 | ||||||
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Title | Transcription initiation complex structures elucidate DNA opening (CC) | ||||||
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![]() | TRANSCRIPTION / GENE EXPRESSION / TRANSCRIPTION INITIATION | ||||||
Function / homology | ![]() RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding ...RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / 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 / RNA Polymerase I Transcription Initiation / DNA binding, bending / 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / acetyltransferase activity / transcription factor TFIID complex / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / disordered domain specific binding / ribosome biogenesis / single-stranded DNA binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / regulation of DNA-templated transcription / nucleolus Similarity search - Function | ||||||
Biological species | ![]() ![]() SYNTHETIC (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å | ||||||
![]() | Plaschka, C. / Hantsche, M. / Dienemann, C. / Burzinski, C. / Plitzko, J. / Cramer, P. | ||||||
![]() | ![]() 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. |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 856.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 144.3 KB | Display | |
Data in CIF | ![]() | 220.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3383MC ![]() 3375C ![]() 3376C ![]() 3377C ![]() 3378C ![]() 3379C ![]() 3380C ![]() 3381C ![]() 3382C ![]() 5fywC ![]() 5ip7C ![]() 5ip9C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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.) ![]() ![]() Plasmid: POPINE / Production host: ![]() ![]() |
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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.) ![]() ![]() Plasmid: PET21B / Production host: ![]() ![]() |
-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) ![]() ![]() |
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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.) ![]() ![]() Plasmid: PET21 / Production host: ![]() ![]() |
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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.) ![]() ![]() Plasmid: PETDUET-1 / Production host: ![]() ![]() |
-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.) ![]() ![]() Strain: BJ5464 RPB3 HIS-BIO / Production host: ![]() ![]() |
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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.) ![]() ![]() Plasmid: POPINE / Production host: ![]() ![]() |
-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.) ![]() ![]() Plasmid: POPINE / Production host: ![]() ![]() |
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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.) ![]() ![]() Plasmid: PET21 / Production host: ![]() ![]() |
-Non-polymers , 2 types, 11 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#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 |
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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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
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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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