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Open data
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Basic information
Entry | Database: PDB / ID: 8h7g | ||||||
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Title | Cryo-EM structure of the human SAGA complex | ||||||
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![]() | TRANSCRIPTION / epigenetics | ||||||
Function / homology | ![]() SAGA-type complex / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / Swr1 complex / negative regulation of microtubule depolymerization ...SAGA-type complex / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / Swr1 complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / splicing factor binding / regulation of double-strand break repair / positive regulation of response to cytokine stimulus / U12-type spliceosomal complex / maintenance of protein location in nucleus / RNA splicing, via transesterification reactions / C2H2 zinc finger domain binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / RNA polymerase binding / limb development / box C/D snoRNP assembly / U2 snRNP / SAGA complex / transcription preinitiation complex / response to L-glutamate / 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 / NuA4 histone acetyltransferase complex / 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 / RNA polymerase II transcribes snRNA genes / MLL1 complex / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / visual perception / TBP-class protein binding / catalytic step 2 spliceosome / response to interleukin-1 / 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 / Formation of the beta-catenin:TCF transactivating complex / spliceosomal complex / multicellular organism growth / G1/S transition of mitotic cell cycle / p53 binding / nuclear matrix / microtubule cytoskeleton organization / autophagy / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / nucleosome / chromatin organization / ATPase binding / HATs acetylate histones / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / regulation of apoptotic process / transcription coactivator activity / transcription cis-regulatory region binding / transcription by RNA polymerase II / chromatin remodeling / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / nuclear speck / protein heterodimerization activity / DNA repair / focal adhesion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
![]() | Huang, J. / Zhang, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Cryo-EM structure of human SAGA transcriptional coactivator complex. Authors: Yuzhu Zhang / Changping Yin / Yue Yin / Mengqi Wei / Wei Jing / Chao Peng / Zhengjun Chen / Jing Huang / ![]() | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 955.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 171.1 KB | Display | |
Data in CIF | ![]() | 261.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34520MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 6 types, 6 molecules CGHIKL
#1: Protein | Mass: 438139.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#6: Protein | Mass: 41797.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Author stated that the 1-39 residues in entity 6 is from the 3xFlag tag and a 3C protease cleavage site Source: (gene. exp.) ![]() ![]() |
#7: Protein | Mass: 66223.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 50705.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Author stated that a twin-strep tag and a TEV cleavage site was included C-terminal Source: (gene. exp.) ![]() ![]() |
#9: Protein | Mass: 67903.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 95597.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3B subunit ... , 2 types, 2 molecules AB
#2: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Transcription ... , 5 types, 5 molecules DEMOR
#4: Protein | Mass: 85884.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: Protein | Mass: 35840.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 29006.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 17948.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 1 molecules X
#13: Protein/peptide | Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author stated that the EM density could not allow model building with confident chain identity Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: human SAGA transcriptional coactivator complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 1.4 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 378168 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.07 Å2 | ||||||||||||||||||||||||
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