[English] 日本語
Yorodumi
- PDB-6tb4: Structure of SAGA bound to TBP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tb4
TitleStructure of SAGA bound to TBP
Components
  • (Subunit of the SAGA ...) x 2
  • (Transcriptional ...) x 2
  • SAGA-associated factor 73 (Sgf73)
  • Spt20
  • Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
  • Subunit (60 kDa) of TFIID and SAGA complexes
  • Subunit (61/68 kDa) of TFIID and SAGA complexes
  • Subunit (90 kDa) of TFIID and SAGA complexes
  • TATA-box Binding Protein (TBP)
  • Transcription initiation factor TFIID subunit 10
  • Transcription-associated protein
KeywordsTRANSCRIPTION / Transcriptional co-activator / Histone-acetylation
Function / homology
Function and homology information


regulation of biosynthetic process / RNA polymerase I transcription regulator complex / RITS complex assembly / positive regulation of DNA-templated transcription initiation / regulatory ncRNA-mediated heterochromatin formation / RNA polymerase III type 3 promoter sequence-specific DNA binding / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex ...regulation of biosynthetic process / RNA polymerase I transcription regulator complex / RITS complex assembly / positive regulation of DNA-templated transcription initiation / regulatory ncRNA-mediated heterochromatin formation / RNA polymerase III type 3 promoter sequence-specific DNA binding / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / NuA4 histone acetyltransferase complex / transcription initiation at RNA polymerase I promoter / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / chromatin organization / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcriptional activator Spt7 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / SAGA-associated factor 73 / LisH / SCA7 domain / SCA7, zinc-binding domain ...Transcriptional activator Spt7 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / SAGA-associated factor 73 / LisH / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / TATA-Binding Protein / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / : / Transcription initiation factor IID, 31kD subunit / 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 / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / : / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Histone, subunit A / Histone, subunit A / TBP domain superfamily / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 10 / TATA-binding protein, general transcription factor / Transcription-associated protein / Spt20-like SEP domain-containing protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Protein SPT3 ...Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 10 / TATA-binding protein, general transcription factor / Transcription-associated protein / Spt20-like SEP domain-containing protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Protein SPT3 / Transcription initiation factor TFIID subunit 5 / Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
Komagataella phaffii GS115 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsPapai, G. / Frechard, A. / Kolesnikova, O. / Crucifix, C. / Schultz, P. / Ben-Shem, A.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0022-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02 France
CitationJournal: Nature / Year: 2020
Title: Structure of SAGA and mechanism of TBP deposition on gene promoters.
Authors: Gabor Papai / Alexandre Frechard / Olga Kolesnikova / Corinne Crucifix / Patrick Schultz / Adam Ben-Shem /
Abstract: SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to ...SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes. Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 Å resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression.
History
DepositionOct 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 30, 2021Group: Source and taxonomy
Category: em_entity_assembly_naturalsource / entity_src_gen / entity_src_nat
Item: _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism ..._em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain
Revision 1.3May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10438
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: TATA-box Binding Protein (TBP)
A: Transcriptional coactivator HFI1/ADA1
C: SAGA-associated factor 73 (Sgf73)
F: Spt20
D: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act
E: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
J: Transcription initiation factor TFIID subunit 10
K: Subunit (61/68 kDa) of TFIID and SAGA complexes
G: Subunit (90 kDa) of TFIID and SAGA complexes
H: Subunit (60 kDa) of TFIID and SAGA complexes
I: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
L: Transcription-associated protein
B: Transcriptional adapter 3 (Ada3)


Theoretical massNumber of molelcules
Total (without water)1,080,38013
Polymers1,080,38013
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area68760 Å2
ΔGint-374 kcal/mol
Surface area248140 Å2
MethodPISA

-
Components

-
Protein , 9 types, 9 molecules MCFJKGHIL

#1: Protein TATA-box Binding Protein (TBP)


Mass: 26931.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: C4QXP3*PLUS
#3: Protein SAGA-associated factor 73 (Sgf73)


Mass: 79995.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: C4QZ39*PLUS
#4: Protein Spt20


Mass: 59530.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZ05
#7: Protein Transcription initiation factor TFIID subunit 10


Mass: 23879.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QXP2
#8: Protein Subunit (61/68 kDa) of TFIID and SAGA complexes


Mass: 66690.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R150
#9: Protein Subunit (90 kDa) of TFIID and SAGA complexes


Mass: 80933.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R4L4
#10: Protein Subunit (60 kDa) of TFIID and SAGA complexes


Mass: 54888.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QW33
#11: Protein Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation


Mass: 17303.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZS5
#12: Protein Transcription-associated protein


Mass: 438055.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QYV4

-
Transcriptional ... , 2 types, 2 molecules AB

#2: Protein Transcriptional coactivator HFI1/ADA1


Mass: 49888.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZA3
#13: Protein Transcriptional adapter 3 (Ada3)


Mass: 6485.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864

-
Subunit of the SAGA ... , 2 types, 2 molecules DE

#5: Protein Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act


Mass: 39030.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3E4
#6: Protein Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex


Mass: 136768.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R5C7

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SAGA bound to TBPCOMPLEXall0MULTIPLE SOURCES
2TATA-box Binding Protein (TBP)COMPLEX#11RECOMBINANT
3SAGA complexCOMPLEX#2-#131NATURAL
Molecular weightValue: 1.6 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Komagataella phaffii GS115 (fungus)644223
23Komagataella phaffii GS115 (fungus)644223
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

-
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 magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 0.8 nm / Calibrated defocus max: 4.5 nm / Cs: 0.01 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 52.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
2SerialEM3.8 betaimage acquisition
4WarpCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1068534
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354104 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more