+Open data
-Basic information
Entry | Database: PDB / ID: 8cll | ||||||
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Title | Structural insights into human TFIIIC promoter recognition | ||||||
Components |
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Keywords | TRANSCRIPTION / TFIIIC / tRNA gene / B-Box promoter / DNA recognition | ||||||
Function / homology | Function and homology information tRNA transcription / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / rRNA transcription / transcription by RNA polymerase III ...tRNA transcription / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / rRNA transcription / transcription by RNA polymerase III / tRNA transcription by RNA polymerase III / histone acetyltransferase activity / histone acetyltransferase / enzyme activator activity / ribonucleoprotein complex / nucleolus / mitochondrion / DNA binding / nucleoplasm / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Seifert-Davila, W. / Girbig, M. / Hauptmann, L. / Hoffmann, T. / Eustermann, S. / Mueller, C.W. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structural insights into human TFIIIC promoter recognition. Authors: Wolfram Seifert-Davila / Mathias Girbig / Luis Hauptmann / Thomas Hoffmann / Sebastian Eustermann / Christoph W Müller / Abstract: Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB ...Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB is the first critical step for tRNA synthesis but is mechanistically poorly understood. Here, we report cryo-electron microscopy structures of the six-subunit human TFIIIC complex unbound and bound to a tRNA gene. The τB module recognizes the B-box via DNA shape and sequence readout through the assembly of multiple winged-helix domains. TFIIIC220 forms an integral part of both τA and τB connecting the two subcomplexes via a ~550-amino acid residue flexible linker. Our data provide a structural mechanism by which high-affinity B-box recognition anchors TFIIIC to promoter DNA and permits scanning for low-affinity A-boxes and TFIIIB for Pol III activation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cll.cif.gz | 710.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cll.ent.gz | 528.8 KB | Display | PDB format |
PDBx/mmJSON format | 8cll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cll_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8cll_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8cll_validation.xml.gz | 87.9 KB | Display | |
Data in CIF | 8cll_validation.cif.gz | 133.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/8cll ftp://data.pdbj.org/pub/pdb/validation_reports/cl/8cll | HTTPS FTP |
-Related structure data
Related structure data | 16717MC 8cliC 8cljC 8clkC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 244200.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12789 #2: Protein | Mass: 92093.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UKN8, histone acetyltransferase #3: Protein | Mass: 102612.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C2, KIAA0011 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WUA4 #4: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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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: TFIIIC tauB Dimer / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.56 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 42.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125600 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.13 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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