[English] 日本語
Yorodumi
- EMDB-10446: SAGA-TBP filtered to show the position of the DUB domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10446
TitleSAGA-TBP filtered to show the position of the DUB domain
Map data
SampleSAGA bound to TBP
  • TATA-box binding protein (TBP)
  • SAGA
  • TATA-binding protein
  • (Transcriptional ...Transcription (biology)) x 2
  • Subunit of SAGA histone acetyltransferase complex
  • Spt20
  • (Subunit of the SAGA ...) x 2
  • (Transcription ...) x 2
  • Subunit (61/68 kDa) of TFIID and SAGA complexes
  • Subunit (90 kDa) of TFIID and SAGA complexes
  • Subunit (60 kDa) of TFIID and SAGA complexes
  • Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
  • Transcription-associated protein
  • Spt8
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase
  • SAGA-associated factor 11
  • ligand
Function / homology
Function and homology information


SAGA-type complex / DUBm complex / nuclear retention of pre-mRNA at the site of transcription / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SAGA complex / transcription export complex 2 / histone H3-K79 methylation / histone deubiquitination / poly(A)+ mRNA export from nucleus ...SAGA-type complex / DUBm complex / nuclear retention of pre-mRNA at the site of transcription / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SAGA complex / transcription export complex 2 / histone H3-K79 methylation / histone deubiquitination / poly(A)+ mRNA export from nucleus / Ada2/Gcn5/Ada3 transcription activator complex / histone H3-K4 methylation / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / molecular adaptor activity / histone acetyltransferase complex / transcription coregulator activity / histone acetylation / transcription elongation from RNA polymerase II promoter / thiol-dependent ubiquitin-specific protease activity / nuclear pore / histone acetyltransferase activity / ubiquitinyl hydrolase 1 / RNA polymerase II activating transcription factor binding / DNA-templated transcription, initiation / enzyme activator activity / regulation of protein localization / P-body / transcription by RNA polymerase II / transferase activity / ubiquitin-dependent protein catabolic process / transcription coactivator activity / regulation of transcription by RNA polymerase II / chromatin binding / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / identical protein binding / nucleus / cytosol
LIS1 homology motif / Histone-fold / Ubiquitin-like domain / TATA-box binding protein / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Bromodomain / Zinc finger, UBP-type / WD40 repeat / PIK-related kinase, FAT / FATC domain ...LIS1 homology motif / Histone-fold / Ubiquitin-like domain / TATA-box binding protein / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Bromodomain / Zinc finger, UBP-type / WD40 repeat / PIK-related kinase, FAT / FATC domain / Transcription initiation factor TAFII31 / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TFIID subunit 12 domain / Transcription initiation factor TFIID, 23-30kDa subunit / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Protein kinase-like domain superfamily / G-protein beta WD-40 repeat / WD40-repeat-containing domain / Ubiquitin conserved site / WD40 repeat, conserved site / Histone acetyltransferases subunit 3 / Transcription factor, enhancer of yellow 2 / Bromodomain, conserved site / Ubiquitin specific protease, conserved site / Armadillo-type fold / TAF6, C-terminal HEAT repeat domain / WD40/YVTN repeat-like-containing domain superfamily / PIK-related kinase / SAGA complex, Sgf11 subunit / SCA7 domain / Zinc finger, RING/FYVE/PHD-type / TBP domain superfamily / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ubiquitin domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 5 / TFIID subunit TAF5, NTD2 domain superfamily / Bromodomain-like superfamily / Transcription factor EnY2 superfamily / WD40-repeat-containing domain superfamily / TATA-box binding protein, eukaryotic / Transcription-associated protein 1 / Papain-like cysteine peptidase superfamily / Transcription initiation factor TFIID subunit 6 / TATA-box binding protein, conserved site / SAGA-associated factor 73 / Ubiquitin-like domain superfamily / Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin specific protease domain / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcription factor Spt20 / Transcriptional activator Spt7
Transcription and mRNA export factor SUS1 / TATA-binding protein / Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex / Subunit (90 kDa) of TFIID and SAGA complexes / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act / SAGA-associated factor 11 / Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / Subunit of SAGA histone acetyltransferase complex / Subunit (61/68 kDa) of TFIID and SAGA complexes / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation ...Transcription and mRNA export factor SUS1 / TATA-binding protein / Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex / Subunit (90 kDa) of TFIID and SAGA complexes / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act / SAGA-associated factor 11 / Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / Subunit of SAGA histone acetyltransferase complex / Subunit (61/68 kDa) of TFIID and SAGA complexes / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation / Transcriptional coactivator HFI1/ADA1 / Uncharacterized protein / Transcription-associated protein / Ubiquitin carboxyl-terminal hydrolase / Transcription initiation factor TFIID subunit 10 / Subunit (60 kDa) of TFIID and SAGA complexes / Polyubiquitin-B
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Komagataella phaffii GS115 (fungus) / Homo sapiens (human) / Yeast (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsPapai G / Frechard A / Kolesnikova O / Crucifix C / Schultz P / Ben-Shem A
Funding support France, 3 items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0022-01 France
French National Research AgencyANR-10-IDEX-0002-02 France
French National Research AgencyANR-10-LABX-0030-INRT 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.
Validation ReportPDB-ID: 6tbm

SummaryFull reportAbout validation report
History
DepositionNov 1, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6tbm
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_10446.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 256 pix.
= 558.08 Å
2.18 Å/pix.
x 256 pix.
= 558.08 Å
2.18 Å/pix.
x 256 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.023929587 - 0.031576734
Average (Standard dev.)0.0000095512 (±0.0011494906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0240.0320.000

-
Supplemental data

-
Sample components

+
Entire SAGA bound to TBP

EntireName: SAGA bound to TBP / Number of components: 24

+
Component #1: protein, SAGA bound to TBP

ProteinName: SAGA bound to TBP / Recombinant expression: No
MassExperimental: 1.6 MDa

+
Component #2: protein, TATA-box binding protein (TBP)

ProteinName: TATA-box binding protein (TBP) / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #3: protein, SAGA bound to TBP

ProteinName: SAGA bound to TBP / Recombinant expression: No
SourceSpecies: Komagataella phaffii GS115 (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, SAGA bound to TBP

ProteinName: SAGA bound to TBP / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #5: protein, SAGA

ProteinName: SAGA / Recombinant expression: No
SourceSpecies: Komagataella phaffii GS115 (fungus)

+
Component #6: protein, TATA-binding protein

ProteinName: TATA-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.042275 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #7: protein, Transcriptional coactivator HFI1/ADA1

ProteinName: Transcriptional coactivator HFI1/ADA1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.888273 kDa
SourceSpecies: Yeast (fungus)

+
Component #8: protein, Subunit of SAGA histone acetyltransferase complex

ProteinName: Subunit of SAGA histone acetyltransferase complex / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 79.995227 kDa
SourceSpecies: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #9: protein, Spt20

ProteinName: Spt20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.530578 kDa
SourceSpecies: Yeast (fungus)

+
Component #10: protein, Subunit of the SAGA and SAGA-like transcriptional regula...

ProteinName: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.030105 kDa
SourceSpecies: Yeast (fungus)

+
Component #11: protein, Subunit of the SAGA transcriptional regulatory complex, ...

ProteinName: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 136.768828 kDa
SourceSpecies: Yeast (fungus)

+
Component #12: protein, Transcription initiation factor TFIID subunit 10

ProteinName: Transcription initiation factor TFIID subunit 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.879145 kDa
SourceSpecies: Yeast (fungus)

+
Component #13: protein, Subunit (61/68 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (61/68 kDa) of TFIID and SAGA complexes / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.690133 kDa
SourceSpecies: Yeast (fungus)

+
Component #14: protein, Subunit (90 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (90 kDa) of TFIID and SAGA complexes / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 80.933008 kDa
SourceSpecies: Yeast (fungus)

+
Component #15: protein, Subunit (60 kDa) of TFIID and SAGA complexes

ProteinName: Subunit (60 kDa) of TFIID and SAGA complexes / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.888445 kDa
SourceSpecies: Yeast (fungus)

+
Component #16: protein, Subunit (17 kDa) of TFIID and SAGA complexes, involved i...

ProteinName: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.303576 kDa
SourceSpecies: Yeast (fungus)

+
Component #17: protein, Transcription-associated protein

ProteinName: Transcription-associated protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 438.055344 kDa
SourceSpecies: Yeast (fungus)

+
Component #18: protein, Transcriptional regulator involved in glucose repression...

ProteinName: Transcriptional regulator involved in glucose repression of Gal4p-regulated genes
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.864305 kDa
SourceSpecies: Yeast (fungus)

+
Component #19: protein, Spt8

ProteinName: Spt8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.059902 kDa
SourceSpecies: Komagataella phaffii GS115 (fungus)

+
Component #20: protein, Polyubiquitin-B

ProteinName: Polyubiquitin-B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.560831 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #21: protein, Ubiquitin carboxyl-terminal hydrolase

ProteinName: Ubiquitin carboxyl-terminal hydrolase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.745879 kDa
SourceSpecies: Yeast (fungus)

+
Component #22: protein, SAGA-associated factor 11

ProteinName: SAGA-associated factor 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.977742 kDa
SourceSpecies: Yeast (fungus)

+
Component #23: protein, Transcription and mRNA export factor SUS1

ProteinName: Transcription and mRNA export factor SUS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.126675 kDa
SourceSpecies: Yeast (fungus)

+
Component #24: ligand, water

LigandName: water / Number of Copies: 91 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 95 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 52.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 354104
3D reconstructionSoftware: RELION / Resolution: 20 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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