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Yorodumi- EMDB-23028: Negative stain EM structure of the human SAGA coactivator complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23028 | |||||||||||||||||||||
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Title | Negative stain EM structure of the human SAGA coactivator complex (TRRAP, core, splicing module) | |||||||||||||||||||||
Map data | map | |||||||||||||||||||||
Sample |
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Keywords | splicing / gene regulation / transcription / chromatin | |||||||||||||||||||||
Function / homology | Function and homology information 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 / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization ...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 / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / splicing factor binding / U12-type spliceosomal complex / maintenance of protein location in nucleus / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / RNA polymerase binding / limb development / U2 snRNP / SAGA complex / transcription preinitiation complex / embryonic placenta development / transcription factor TFIID complex / precatalytic spliceosome / RNA polymerase II general transcription initiation factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nucleus organization / 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 / mRNA Splicing - Minor Pathway / regulation of RNA splicing / histone deacetylase complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / male germ cell nucleus / U2 snRNA binding / somitogenesis / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / gastrulation / RNA Polymerase II Pre-transcription Events / visual perception / TBP-class protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / negative regulation of protein catabolic process / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / spliceosomal complex / multicellular organism growth / G1/S transition of mitotic cell cycle / nuclear matrix / microtubule cytoskeleton organization / autophagy / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / transcription corepressor activity / microtubule cytoskeleton / positive regulation of cell growth / HATs acetylate histones / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription coactivator activity / transcription by RNA polymerase II / chromatin remodeling / protein stabilization / Ub-specific processing proteases / nuclear speck / protein heterodimerization activity / focal adhesion / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / unclassified Rhodococcus (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.09 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_23028.map.gz | 94.1 MB | EMDB map data format | |
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Header (meta data) | emd-23028-v30.xml emd-23028.xml | 47.5 KB 47.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23028_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_23028.png | 74.3 KB | ||
Masks | emd_23028_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-23028.cif.gz | 13.3 KB | ||
Others | emd_23028_half_map_1.map.gz emd_23028_half_map_2.map.gz | 80.8 MB 80.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23028 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23028 | HTTPS FTP |
-Validation report
Summary document | emd_23028_validation.pdf.gz | 860.4 KB | Display | EMDB validaton report |
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Full document | emd_23028_full_validation.pdf.gz | 859.9 KB | Display | |
Data in XML | emd_23028_validation.xml.gz | 17 KB | Display | |
Data in CIF | emd_23028_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23028 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23028 | HTTPS FTP |
-Related structure data
Related structure data | 7ktsMC 7ktrC 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_23028.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 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_23028_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_23028_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_23028_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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 gam...
+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: Splicing factor 3B subunit 3
+Macromolecule #13: Splicing factor 3B subunit 5
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: Buffers were freshly prepared and 0.22 um filtered. | ||||||||||||||||||
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Staining | Type: NEGATIVE / Material: uranyl formate | ||||||||||||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | ||||||||||||||||||
Details | The sample was crosslinked with 1 mM bis(sulfosuccinimidyl)suberate (BS3) prior to freezing |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 745 / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | PDB-7kts: |