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Yorodumi- EMDB-23027: Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23027 | |||||||||||||||||||||
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Title | Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) | |||||||||||||||||||||
Map data | LocSpiral filtered map | |||||||||||||||||||||
Sample |
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Keywords | coactivator / gene regulation / transcription / chromatin | |||||||||||||||||||||
Function / homology | Function and homology information regulation of macromolecule metabolic process / SAGA-type complex / regulation of primary metabolic process / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / negative regulation of microtubule depolymerization ...regulation of macromolecule metabolic process / SAGA-type complex / regulation of primary metabolic process / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / negative regulation of microtubule depolymerization / SLIK (SAGA-like) complex / hepatocyte differentiation / maintenance of protein location in nucleus / RNA polymerase binding / SAGA complex / limb development / transcription preinitiation complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / nucleus organization / 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 / histone deacetylase complex / histone acetyltransferase complex / somitogenesis / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / gastrulation / RNA Polymerase II Pre-transcription Events / visual perception / TBP-class protein binding / male germ cell nucleus / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / nuclear estrogen receptor binding / promoter-specific chromatin binding / transcription coregulator activity / mRNA transcription by RNA polymerase II / multicellular organism growth / autophagy / microtubule cytoskeleton organization / nuclear matrix / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / transcription corepressor activity / microtubule cytoskeleton / HATs acetylate histones / positive regulation of cell growth / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / Ub-specific processing proteases / nuclear speck / chromatin remodeling / protein heterodimerization activity / focal adhesion / regulation of DNA-templated transcription / negative regulation of apoptotic process / nucleolus / regulation of transcription by RNA polymerase II / apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / unclassified Rhodococcus (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.93 Å | |||||||||||||||||||||
Authors | Herbst DA / Esbin MN | |||||||||||||||||||||
Funding support | United States, European Union, Switzerland, 6 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structure of the human SAGA coactivator complex. Authors: Dominik A Herbst / Meagan N Esbin / Robert K Louder / Claire Dugast-Darzacq / Gina M Dailey / Qianglin Fang / Xavier Darzacq / Robert Tjian / Eva Nogales / Abstract: The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are ...The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23027.map.gz | 15.8 MB | EMDB map data format | |
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Header (meta data) | emd-23027-v30.xml emd-23027.xml | 47.6 KB 47.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23027_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_23027.png | 130.6 KB | ||
Masks | emd_23027_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-23027.cif.gz | 12.7 KB | ||
Others | emd_23027_additional_1.map.gz emd_23027_additional_2.map.gz emd_23027_additional_3.map.gz emd_23027_half_map_1.map.gz emd_23027_half_map_2.map.gz | 20.5 MB 21 MB 166.7 MB 140.9 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23027 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23027 | HTTPS FTP |
-Validation report
Summary document | emd_23027_validation.pdf.gz | 976.5 KB | Display | EMDB validaton report |
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Full document | emd_23027_full_validation.pdf.gz | 976 KB | Display | |
Data in XML | emd_23027_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_23027_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23027 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23027 | HTTPS FTP |
-Related structure data
Related structure data | 7ktrMC 7ktsC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23027.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | LocSpiral filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.187 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23027_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: LocSpiral filtered multibody map of the TRRAP module
File | emd_23027_additional_1.map | ||||||||||||
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Annotation | LocSpiral filtered multibody map of the TRRAP module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: LocSpiral filtered multibody map of the core module
File | emd_23027_additional_2.map | ||||||||||||
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Annotation | LocSpiral filtered multibody map of the core module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Relion postprocessed map
File | emd_23027_additional_3.map | ||||||||||||
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Annotation | Relion postprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_23027_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_23027_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human SAGA
+Supramolecule #1: human SAGA
+Supramolecule #2: human SAGA
+Supramolecule #3: STAGA complex 65 subunit gamma
+Macromolecule #1: Transformation/transcription domain-associated protein,Transforma...
+Macromolecule #2: TAF5-like RNA polymerase II p300/CBP-associated factor-associated...
+Macromolecule #3: Isoform 3 of Transcription factor SPT20 homolog
+Macromolecule #4: STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamm...
+Macromolecule #5: Transcription initiation factor TFIID subunit 9B
+Macromolecule #6: TAF6-like RNA polymerase II p300/CBP-associated factor-associated...
+Macromolecule #7: Transcription initiation factor TFIID subunit 12
+Macromolecule #8: Transcription initiation factor TFIID subunit 10
+Macromolecule #9: Transcription initiation protein SPT3 homolog,Transcription initi...
+Macromolecule #10: Transcriptional adapter 1
+Macromolecule #11: Ataxin-7
+Macromolecule #12: INOSITOL HEXAKISPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 Component:
Details: Buffers were freshly prepared and 0.22 um filtered. | |||||||||||||||||||||
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 59 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blot time 3 sec. | |||||||||||||||||||||
Details | The sample was crosslinked with 1 mM bis(sulfosuccinimidyl)suberate (BS3) prior to freezing |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10224 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7ktr: |