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- PDB-6mzc: Human TFIID BC core -

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Basic information

Entry
Database: PDB / ID: 6mzc
TitleHuman TFIID BC core
Components
  • (Transcription initiation factor TFIID subunit ...) x 9
  • poly(UNK)
KeywordsTRANSCRIPTION / DNA / Nuclear
Function / homology
Function and homology information


SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / hepatocyte differentiation / positive regulation of response to cytokine stimulus / maintenance of protein location in nucleus ...SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / hepatocyte differentiation / positive regulation of response to cytokine stimulus / maintenance of protein location in nucleus / C2H2 zinc finger domain binding / box C/D snoRNP assembly / RNA polymerase binding / regulation of fat cell differentiation / limb development / SAGA complex / transcription preinitiation complex / inner cell mass cell proliferation / response to L-glutamate / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / regulation of RNA splicing / aryl hydrocarbon receptor binding / MLL1 complex / negative regulation of cell cycle / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / somitogenesis / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / male germ cell nucleus / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / : / multicellular organism growth / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / p53 binding / actin cytoskeleton / HATs acetylate histones / ATPase binding / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / cell differentiation / transcription coactivator activity / transcription cis-regulatory region binding / protein stabilization / Ub-specific processing proteases / positive regulation of apoptotic process / chromatin remodeling / protein heterodimerization activity / negative regulation of cell population proliferation / apoptotic process / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. ...Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / : / Transcription initiation factor IID, 31kD subunit / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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
Transcription initiation factor TFIID subunit 4 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsPatel, A.B. / Louder, R.K. / Greber, B.J. / Grunberg, S. / Luo, J. / Fang, J. / Liu, Y. / Ranish, J. / Hahn, S. / Nogales, E.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM63072 United States
CitationJournal: Science / Year: 2018
Title: Structure of human TFIID and mechanism of TBP loading onto promoter DNA.
Authors: Avinash B Patel / Robert K Louder / Basil J Greber / Sebastian Grünberg / Jie Luo / Jie Fang / Yutong Liu / Jeff Ranish / Steve Hahn / Eva Nogales /
Abstract: The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and ...The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo-electron microscopy, chemical cross-linking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA box-binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter.
History
DepositionNov 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 28, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type
Revision 1.5May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
B: Transcription initiation factor TFIID subunit 2
E: Transcription initiation factor TFIID subunit 4
G: Transcription initiation factor TFIID subunit 5
H: Transcription initiation factor TFIID subunit 6
I: Transcription initiation factor TFIID subunit 6
K: Transcription initiation factor TFIID subunit 8
M: Transcription initiation factor TFIID subunit 9
O: Transcription initiation factor TFIID subunit 10
R: Transcription initiation factor TFIID subunit 12
Z: poly(UNK)


Theoretical massNumber of molelcules
Total (without water)600,04110
Polymers600,04110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcription initiation factor TFIID subunit ... , 9 types, 9 molecules BEGHIKMOR

#1: Protein Transcription initiation factor TFIID subunit 2 / 150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B / TBP- ...150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B / TBP-associated factor 150 kDa


Mass: 137159.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q6P1X5
#2: Protein Transcription initiation factor TFIID subunit 4 / RNA polymerase II TBP-associated factor subunit C / TBP-associated factor 4 / Transcription ...RNA polymerase II TBP-associated factor subunit C / TBP-associated factor 4 / Transcription initiation factor TFIID 130 kDa subunit


Mass: 110221.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00268
#3: Protein Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID 100 kDa subunit / TAFII100


Mass: 85785.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15542
#4: Protein Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa ...RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa subunit / TAFII70 / Transcription initiation factor TFIID 80 kDa subunit / TAFII80


Mass: 72749.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#5: Protein Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa ...RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa subunit / TAFII70 / Transcription initiation factor TFIID 80 kDa subunit


Mass: 72365.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49848
#6: Protein Transcription initiation factor TFIID subunit 8 / Protein taube nuss / TBP-associated factor 43 kDa


Mass: 32975.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7C8
#7: Protein Transcription initiation factor TFIID subunit 9 / RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor ...RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor TFIID 31 kDa subunit / TAFII31 / Transcription initiation factor TFIID 32 kDa subunit


Mass: 28830.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594
#8: Protein Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAFII30


Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962
#9: Protein Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII20/TAFII15


Mass: 17948.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514

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Protein , 1 types, 1 molecules Z

#10: Protein poly(UNK)


Mass: 20272.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Details

Has protein modificationN

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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: General transcription factor IID / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa
Buffer solutionpH: 7.9
Buffer component
IDConc.FormulaBuffer-ID
120 mMHEPES1
2.1 mMEDTA1
35 mMMgCl1
42 %Glycerol1
51 %Trehalose1
6100 mMKCl1
7.01 %NP-401
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Treated with PEI
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: BT 4s; BF 15N

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3211: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4GctfCTF correction
8PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266328 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0121660
ELECTRON MICROSCOPYf_angle_d1.29129451
ELECTRON MICROSCOPYf_dihedral_angle_d8.06713060
ELECTRON MICROSCOPYf_chiral_restr0.0653434
ELECTRON MICROSCOPYf_plane_restr0.0093799

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