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- PDB-8cli: TFIIIC TauB-DNA monomer -

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Basic information

Entry
Database: PDB / ID: 8cli
TitleTFIIIC TauB-DNA monomer
Components
  • (DNA (35-MER)) x 2
  • (General transcription factor 3C polypeptide ...) x 3
KeywordsTRANSCRIPTION / 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 / histone H3K14 acetyltransferase activity / 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 ...tRNA transcription / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / histone H3K14 acetyltransferase activity / 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 / histone acetyltransferase / tRNA transcription by RNA polymerase III / ribonucleoprotein complex / nucleolus / mitochondrion / DNA binding / nucleoplasm / membrane
Similarity search - Function
Transcription factor IIIC, 90kDa subunit, N-terminal / General transcription factor 3C polypeptide 4 / Domain of unknown function DUF5921 / Transcription factor IIIC subunit delta bet-propeller domain / Domain of unknown function (DUF5921) / : / : / General transcription factor 3C polypeptide 1, winged-helix domain / GTF3C1, extended winged-helix domain / Transcription factor IIIC, putative zinc-finger ...Transcription factor IIIC, 90kDa subunit, N-terminal / General transcription factor 3C polypeptide 4 / Domain of unknown function DUF5921 / Transcription factor IIIC subunit delta bet-propeller domain / Domain of unknown function (DUF5921) / : / : / General transcription factor 3C polypeptide 1, winged-helix domain / GTF3C1, extended winged-helix domain / Transcription factor IIIC, putative zinc-finger / : / Putative zinc-finger of transcription factor IIIC complex / B-block binding subunit of TFIIIC / Tfc3, extended winged-helix domain / Transcription facto Tfc3-like / B-block binding subunit of TFIIIC / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / General transcription factor 3C polypeptide 1 / General transcription factor 3C polypeptide 2 / General transcription factor 3C polypeptide 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSeifert-Davila, W. / Girbig, M. / Hauptmann, L. / Hoffmann, T. / Eustermann, S. / Mueller, C.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: 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
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Structure summary / Category: audit_author / citation
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_validate_planes.type
Revision 1.3Jul 24, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_validate_planes
Item: _em_admin.last_update / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcription factor 3C polypeptide 1
B: General transcription factor 3C polypeptide 4
C: General transcription factor 3C polypeptide 2
D: DNA (35-MER)
E: DNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,5757
Polymers460,4445
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Mass photometry shows a TFIIIC-DNA complex with a molecular mass of 701 kDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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General transcription factor 3C polypeptide ... , 3 types, 3 molecules ABC

#1: Protein General transcription factor 3C polypeptide 1 / TF3C-alpha / TFIIIC box B-binding subunit / Transcription factor IIIC 220 kDa subunit / TFIIIC 220 ...TF3C-alpha / TFIIIC box B-binding subunit / Transcription factor IIIC 220 kDa subunit / TFIIIC 220 kDa subunit / TFIIIC220 / Transcription factor IIIC subunit alpha


Mass: 244200.719 Da / Num. of mol.: 1
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 General transcription factor 3C polypeptide 4 / TF3C-delta / Transcription factor IIIC 90 kDa subunit / TFIIIC 90 kDa subunit / TFIIIC90 / ...TF3C-delta / Transcription factor IIIC 90 kDa subunit / TFIIIC 90 kDa subunit / TFIIIC90 / Transcription factor IIIC subunit delta


Mass: 92093.195 Da / Num. of mol.: 1
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 General transcription factor 3C polypeptide 2 / TF3C-beta / Transcription factor IIIC 110 kDa subunit / TFIIIC 110 kDa subunit / TFIIIC110 / ...TF3C-beta / Transcription factor IIIC 110 kDa subunit / TFIIIC 110 kDa subunit / TFIIIC110 / Transcription factor IIIC subunit beta


Mass: 102612.453 Da / Num. of mol.: 1
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

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DNA chain , 2 types, 2 molecules DE

#4: DNA chain DNA (35-MER)


Mass: 10819.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (35-MER)


Mass: 10717.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TFIIIC tauB-DNA monomer / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 42.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35379 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005116430
ELECTRON MICROSCOPYf_angle_d0.726622555
ELECTRON MICROSCOPYf_chiral_restr0.04712504
ELECTRON MICROSCOPYf_plane_restr0.00712632
ELECTRON MICROSCOPYf_dihedral_angle_d18.57552662

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