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- PDB-8h7g: Cryo-EM structure of the human SAGA complex -

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Basic information

Entry
Database: PDB / ID: 8h7g
TitleCryo-EM structure of the human SAGA complex
Components
  • (Splicing factor 3B subunit ...) x 2
  • (Transcription ...) x 5
  • Ataxin-7
  • STAGA complex 65 subunit gamma
  • TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
  • TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
  • Transcriptional adapter 1
  • Transformation/transcription domain-associated protein
  • Unassigned sequence
KeywordsTRANSCRIPTION / epigenetics
Function / homology
Function and homology information


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 / Swr1 complex / SLIK (SAGA-like) 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 / Swr1 complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / splicing factor binding / regulation of double-strand break repair / U12-type spliceosomal complex / positive regulation of response to cytokine stimulus / maintenance of protein location in nucleus / RNA splicing, via transesterification reactions / C2H2 zinc finger domain binding / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / box C/D snoRNP assembly / RNA polymerase binding / limb development / U2 snRNP / transcription preinitiation complex / SAGA complex / response to L-glutamate / precatalytic spliceosome / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / NuA4 histone acetyltransferase complex / 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 / RNA polymerase II transcribes snRNA genes / MLL1 complex / histone acetyltransferase complex / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / positive regulation of double-strand break repair via homologous recombination / somitogenesis / U2 snRNA binding / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / gastrulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / catalytic step 2 spliceosome / visual perception / response to interleukin-1 / mRNA Splicing - Major Pathway / RNA splicing / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / spliceosomal complex / Formation of the beta-catenin:TCF transactivating complex / mRNA transcription by RNA polymerase II / negative regulation of protein catabolic process / multicellular organism growth / mRNA splicing, via spliceosome / autophagy / microtubule cytoskeleton organization / nuclear matrix / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / microtubule cytoskeleton / nucleosome / p53 binding / chromatin organization / HATs acetylate histones / ATPase binding / DNA-binding transcription factor binding / regulation of apoptotic process / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / nuclear speck / chromatin remodeling / protein heterodimerization activity / focal adhesion / DNA repair
Similarity search - Function
STAGA complex 65 subunit gamma / : / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. ...STAGA complex 65 subunit gamma / : / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / 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 / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / : / 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 / Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / : / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / 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 / Histone-fold / Armadillo-like helical / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription factor SPT20 homolog / Transcriptional adapter 1 ...Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Splicing factor 3B subunit 3 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / Splicing factor 3B subunit 5 / Transformation/transcription domain-associated protein / TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHuang, J. / Zhang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2022
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
DepositionOct 20, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Transformation/transcription domain-associated protein
A: Splicing factor 3B subunit 3
B: Splicing factor 3B subunit 5
D: Transcription factor SPT20 homolog
E: Transcription initiation protein SPT3 homolog
G: Transcriptional adapter 1
H: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
I: STAGA complex 65 subunit gamma
K: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
M: Transcription initiation factor TFIID subunit 9
O: Transcription initiation factor TFIID subunit 10
R: Transcription initiation factor TFIID subunit 12
X: Unassigned sequence
L: Ataxin-7


Theoretical massNumber of molelcules
Total (without water)1,098,28114
Polymers1,098,28114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules CGHIKL

#1: Protein Transformation/transcription domain-associated protein / 350/400 kDa PCAF-associated factor / PAF350/400 / STAF40 / Tra1 homolog


Mass: 438139.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y4A5
#6: Protein Transcriptional adapter 1 / SPT3-associated factor 42 / STAF42 / Transcriptional adapter 1-like 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.) Homo sapiens (human) / Gene: TADA1, TADA1L / Production host: Homo sapiens (human) / References: UniProt: Q96BN2
#7: Protein TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / TAF5L / PCAF-associated factor 65 beta / PAF65-beta


Mass: 66223.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75529
#8: Protein STAGA complex 65 subunit gamma / Adenocarcinoma antigen ART1 / SPTF-associated factor 65 gamma / STAF65gamma / Suppressor of Ty 7-like


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.) Homo sapiens (human) / Gene: SUPT7L, KIAA0764 / Production host: Homo sapiens (human) / References: UniProt: O94864
#9: Protein TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L / TAF6L / PCAF-associated factor 65-alpha / PAF65-alpha


Mass: 67903.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6J9
#14: Protein Ataxin-7 / Spinocerebellar ataxia type 7 protein


Mass: 95597.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15265

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Splicing factor 3B subunit ... , 2 types, 2 molecules AB

#2: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393
#3: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5

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Transcription ... , 5 types, 5 molecules DEMOR

#4: Protein Transcription factor SPT20 homolog / p38-interacting protein / p38IP


Mass: 85884.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NEM7
#5: Protein Transcription initiation protein SPT3 homolog / SPT3-like protein


Mass: 35840.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75486
#10: Protein Transcription initiation factor TFIID subunit 9 / RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor ...RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor TFIID 31 kDa subunit / TAFII-31 / TAFII31 / Transcription initiation factor TFIID 32 kDa subunit / TAFII-32 / TAFII32


Mass: 29006.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16594
#11: Protein Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAF(II)30 / TAFII-30 / TAFII30


Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962
#12: Protein Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII-20/TAFII-15 / TAFII20/TAFII15


Mass: 17948.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514

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Protein/peptide , 1 types, 1 molecules X

#13: Protein/peptide Unassigned sequence


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) Homo sapiens (human)

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: human SAGA transcriptional coactivator complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 378168 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002153691
ELECTRON MICROSCOPYf_angle_d0.510772676
ELECTRON MICROSCOPYf_chiral_restr0.03868304
ELECTRON MICROSCOPYf_plane_restr0.0049242
ELECTRON MICROSCOPYf_dihedral_angle_d3.46277102

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