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- PDB-8clj: TFIIIC TauB-DNA dimer -

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Basic information

Entry
Database: PDB / ID: 8clj
TitleTFIIIC TauB-DNA dimer
Components
  • (General transcription factor 3C polypeptide ...) x 3
  • (tDNA (35-MER)) x 2
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_author / Item: _audit_author.name / _citation_author.name
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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_validate_planes.type
Revision 2.0Jul 24, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_admin / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_poly_seq_scheme / pdbx_validate_planes / pdbx_validate_rmsd_angle / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_ref_seq
Item: _atom_site.auth_seq_id / _em_admin.last_update ..._atom_site.auth_seq_id / _em_admin.last_update / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair_step.i_auth_seq_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_2 / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.step_name / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_validate_planes.type / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.dom_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end

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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: tDNA (35-MER)
E: tDNA (35-MER)
F: General transcription factor 3C polypeptide 1
G: General transcription factor 3C polypeptide 4
H: General transcription factor 3C polypeptide 2
I: tDNA (35-MER)
J: tDNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)921,15014
Polymers920,88810
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "A"
d_1ens_2chain "G"
d_2ens_2chain "B"
d_1ens_3chain "H"
d_2ens_3chain "C"
d_1ens_4chain "I"
d_2ens_4chain "D"
d_1ens_5chain "E"
d_2ens_5chain "J"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETASNASNFF1 - 7161 - 716
d_21ens_1METMETASNASNAA1 - 7161 - 716
d_11ens_2METMETPHEPHEGG50 - 82250 - 822
d_12ens_2ZNZNZNZNGM - N901 - 902
d_21ens_2METMETPHEPHEBB50 - 82250 - 822
d_22ens_2ZNZNZNZNBK - L901 - 902
d_21ens_3HISHISGLNGLNHH290 - 890304 - 904
d_11ens_3HISHISGLNGLNCC290 - 890304 - 904
d_11ens_4DADADTDTII1 - 351 - 35
d_21ens_4DADADTDTDD1 - 351 - 35
d_11ens_5DADADTDTJJ1 - 351 - 35
d_21ens_5DADADTDTEE1 - 351 - 35

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(0.177831605165, -0.72665890412, 0.663583270787), (-0.984060036009, -0.130405281984, 0.120914465473), (-0.00132880942573, -0.674508190828, -0.738266167972)207.746138706, 398.255906743, 496.665928173
2given(0.177871234342, -0.72633245141, 0.663929961685), (-0.984053331879, -0.130649826243, 0.120704858725), (-0.000929521802967, -0.674812413143, -0.737988714722)207.630686183, 398.326080802, 496.605548198
3given(0.177753584322, -0.984074670173, -0.000840704502174), (-0.726313611496, -0.130617636609, -0.674838922086), (0.663982078837, 0.120565652364, -0.737964580758)355.513277773, 537.961691099, 180.563726798
4given(0.1778723532, -0.726332235474, 0.663929898166), (-0.984053129914, -0.13065083761, 0.120705410563), (-0.000929233378615, -0.674812449755, -0.737988681608)207.63042214, 398.326155541, 496.605501247
5given(0.177871380733, -0.726332370378, 0.663930011114), (-0.984053305295, -0.13064983341, 0.120705067698), (-0.000929652589821, -0.674812498974, -0.737988636074)207.630617643, 398.326015949, 496.605563769

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Components

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General transcription factor 3C polypeptide ... , 3 types, 6 molecules AFBGCH

#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.: 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 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.: 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 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.: 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

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DNA chain , 2 types, 4 molecules DIEJ

#4: DNA chain tDNA (35-MER)


Mass: 10819.942 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: DNA chain tDNA (35-MER)


Mass: 10717.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 1 types, 4 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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 Dimer / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.6 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
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: 83.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003432860
ELECTRON MICROSCOPYf_angle_d0.719345110
ELECTRON MICROSCOPYf_chiral_restr0.04485008
ELECTRON MICROSCOPYf_plane_restr0.00585264
ELECTRON MICROSCOPYf_dihedral_angle_d18.49435324
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FELECTRON MICROSCOPYNCS constraints2.04418938103E-13
ens_2d_2GELECTRON MICROSCOPYNCS constraints8.5029127574E-12
ens_3d_2CELECTRON MICROSCOPYNCS constraints4.12273182478E-13
ens_4d_2IELECTRON MICROSCOPYNCS constraints1.21702161141E-13
ens_5d_2JELECTRON MICROSCOPYNCS constraints9.768269435E-13

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