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- PDB-8cll: Structural insights into human TFIIIC promoter recognition -

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Basic information

Entry
Database: PDB / ID: 8cll
TitleStructural insights into human TFIIIC promoter recognition
Components
  • General transcription factor 3C polypeptide 1
  • General transcription factor 3C polypeptide 2
  • General transcription factor 3C polypeptide 4
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 / 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 / tRNA transcription by RNA polymerase III / rRNA transcription ...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 / tRNA transcription by RNA polymerase III / rRNA transcription / enzyme activator activity / transcription by RNA polymerase III / histone acetyltransferase activity / histone acetyltransferase / 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) / 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 ...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) / 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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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: 3.4 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 / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_validate_planes / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim
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 / _refine_ls_restr_ncs.pdbx_asym_id / _refine_ls_restr_ncs.pdbx_auth_asym_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.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
Revision 1.3Dec 20, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _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
F: General transcription factor 3C polypeptide 1
G: General transcription factor 3C polypeptide 4
H: General transcription factor 3C polypeptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)878,07410
Polymers877,8136
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "D"
d_1ens_2chain "E"
d_2ens_2chain "B"
d_1ens_3chain "C"
d_2ens_3chain "F"

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_1METMETGLUGLUAA1 - 4201 - 420
d_21ens_1METMETGLUGLUFD1 - 4201 - 420
d_11ens_2METMETPHEPHEBB50 - 82250 - 822
d_12ens_2ZNZNZNZNBG - H901 - 902
d_21ens_2METMETPHEPHEGE50 - 82250 - 822
d_22ens_2ZNZNZNZNGI - J901 - 902
d_11ens_3HISHISGLNGLNCC290 - 890304 - 904
d_21ens_3HISHISGLNGLNHF290 - 890304 - 904

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.0356157254941, -0.996560295403, 0.0748271189003), (-0.728302509438, 0.0771540789697, 0.680898452667), (-0.684329580571, -0.0302460860895, -0.728545262446)383.704605943, 155.035494726, 473.396741302
2given(-0.0338096781676, -0.726830862683, -0.685983821029), (-0.996583041349, 0.0762729582515, -0.0316966486432), (0.0753601178201, 0.682568189187, -0.726926075851)450.09220604, 385.171400197, 209.897849649
3given(-0.0343427048989, -0.728004429345, -0.684711712675), (-0.996205190522, 0.0797597827344, -0.0348366966648), (0.0799737269144, 0.680916975785, -0.727980957918)450.262131696, 384.954639489, 209.578625396

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Components

#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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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 Dimer / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.56 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 FIELDBright-field microscopy / 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125600 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 115.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325880
ELECTRON MICROSCOPYf_angle_d0.660935110
ELECTRON MICROSCOPYf_chiral_restr0.0473834
ELECTRON MICROSCOPYf_plane_restr0.00954496
ELECTRON MICROSCOPYf_dihedral_angle_d12.97229602
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints5.6678364148E-13
ens_2d_2EGELECTRON MICROSCOPYNCS constraints5.54398206481E-13
ens_3d_2CCELECTRON MICROSCOPYNCS constraints2.73569698131E-13

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