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- EMDB-10415: SAGA DUB module bound to a ubiqitinated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-10415
TitleSAGA DUB module bound to a ubiqitinated nucleosome
Map datapostprocess masked map
Sample
  • Complex: SAGA DUB-ubiqitinated nucleosome complex
    • Complex: nucleosome
      • Protein or peptide: x 5 types
    • Complex: SAGA DUB module
      • Protein or peptide: x 3 types
    • Complex: DNA
      • DNA: x 2 types
    • Complex: Ubiquitin carboxyl-terminal hydrolase 8
      • Protein or peptide: x 1 types
    • Complex: ubiquitin
      • Protein or peptide: x 1 types
  • Ligand: x 1 types
KeywordsCoactivator / Transcription / Histone acetyltransferase / Histone deubiquitinase / GENE REGULATION
Function / homology
Function and homology information


RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / Ub-specific processing proteases / nuclear pore / mRNA export from nucleus / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / RNA splicing / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / enzyme activator activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / transcription elongation by RNA polymerase II / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import
Similarity search - Function
Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAGA-associated factor 73 ...Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAGA-associated factor 73 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Papain-like cysteine peptidase superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Ubiquitin conserved site / Core histone H2A/H2B/H3/H4 / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase 8 / SAGA-associated factor 73 / Histone H4 / Histone H3.2 / SAGA-associated factor 11 / Histone H2A / Transcription and mRNA export factor SUS1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang H / Cramer P
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationSFB860, SPP1935, EXC 2067/1-390729940 Germany
European Research Council693023 Germany
CitationJournal: Nature / Year: 2020
Title: Structure of the transcription coactivator SAGA.
Authors: Haibo Wang / Christian Dienemann / Alexandra Stützer / Henning Urlaub / Alan C M Cheung / Patrick Cramer /
Abstract: Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase) and transcription factor IID (TFIID). SAGA is ...Gene transcription by RNA polymerase II is regulated by activator proteins that recruit the coactivator complexes SAGA (Spt-Ada-Gcn5-acetyltransferase) and transcription factor IID (TFIID). SAGA is required for all regulated transcription and is conserved among eukaryotes. SAGA contains four modules: the activator-binding Tra1 module, the core module, the histone acetyltransferase (HAT) module and the histone deubiquitination (DUB) module. Previous studies provided partial structures, but the structure of the central core module is unknown. Here we present the cryo-electron microscopy structure of SAGA from the yeast Saccharomyces cerevisiae and resolve the core module at 3.3 Å resolution. The core module consists of subunits Taf5, Sgf73 and Spt20, and a histone octamer-like fold. The octamer-like fold comprises the heterodimers Taf6-Taf9, Taf10-Spt7 and Taf12-Ada1, and two histone-fold domains in Spt3. Spt3 and the adjacent subunit Spt8 interact with the TATA box-binding protein (TBP). The octamer-like fold and its TBP-interacting region are similar in TFIID, whereas Taf5 and the Taf6 HEAT domain adopt distinct conformations. Taf12 and Spt20 form flexible connections to the Tra1 module, whereas Sgf73 tethers the DUB module. Binding of a nucleosome to SAGA displaces the HAT and DUB modules from the core-module surface, allowing the DUB module to bind one face of an ubiquitinated nucleosome.
History
DepositionOct 28, 2019-
Header (metadata) releaseNov 6, 2019-
Map releaseJan 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t9l
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10415.png

Downloads & links

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Map

FileDownload / File: emd_10415.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess masked map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 400 pix.
= 548. Å		1.37 Å/pix.
x 400 pix.
= 548. Å		1.37 Å/pix.
x 400 pix.
= 548. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.10051431 - 0.22963826
Average (Standard dev.)0.000099417266 (±0.002636907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 548.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z548.000548.000548.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1010.2300.000

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Supplemental data

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Half map: half map 1

Fileemd_10415_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10415_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SAGA DUB-ubiqitinated nucleosome complex

EntireName: SAGA DUB-ubiqitinated nucleosome complex
Components
  • Complex: SAGA DUB-ubiqitinated nucleosome complex
    • Complex: nucleosome
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H2B
    • Complex: SAGA DUB module
      • Protein or peptide: Transcription and mRNA export factor SUS1
      • Protein or peptide: SAGA-associated factor 11
      • Protein or peptide: SAGA-associated factor 73
    • Complex: DNA
      • DNA: Widom601 DNA (145-MER)
      • DNA: Widom601 DNA (145-MER)
    • Complex: Ubiquitin carboxyl-terminal hydrolase 8
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 8
    • Complex: ubiquitin
      • Protein or peptide: Polyubiquitin-C
  • Ligand: ZINC ION

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Supramolecule #1: SAGA DUB-ubiqitinated nucleosome complex

SupramoleculeName: SAGA DUB-ubiqitinated nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Molecular weightTheoretical: 250 KDa

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Supramolecule #2: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: SAGA DUB module

SupramoleculeName: SAGA DUB module / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#11
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)

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Supramolecule #5: Ubiquitin carboxyl-terminal hydrolase 8

SupramoleculeName: Ubiquitin carboxyl-terminal hydrolase 8 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Supramolecule #6: ubiquitin

SupramoleculeName: ubiquitin / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #12
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: UNIPROTKB: F6R8G8

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Macromolecule #8: Ubiquitin carboxyl-terminal hydrolase 8

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 8 / type: protein_or_peptide / ID: 8 / Details: This is a zinc containing protein. / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 53.69227 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSICPHIQQV FQNEKSKDGV LKTCNAARYI LNHSVPKEKF LNTMKCGTCH EINSGATFMC LQCGFCGCWN HSHFLSHSKQ IGHIFGINS NNGLLFCFKC EDYIGNIDLI NDAILAKYWD DVCTKTMVPS MERRDGLSGL INMGSTCFMS SILQCLIHNP Y FIRHSMSQ ...String:
MSICPHIQQV FQNEKSKDGV LKTCNAARYI LNHSVPKEKF LNTMKCGTCH EINSGATFMC LQCGFCGCWN HSHFLSHSKQ IGHIFGINS NNGLLFCFKC EDYIGNIDLI NDAILAKYWD DVCTKTMVPS MERRDGLSGL INMGSTCFMS SILQCLIHNP Y FIRHSMSQ IHSNNCKVRS PDKCFSCALD KIVHELYGAL NTKQASSSST STNRQTGFIY LLTCAWKINQ NLAGYSQQDA HE FWQFIIN QIHQSYVLDL PNAKEVSRAN NKQCECIVHT VFEGSLESSI VCPGCQNNSK TTIDPFLDLS LDIKDKKKLY ECL DSFHKK EQLKDFNYHC GECNSTQDAI KQLGIHKLPS VLVLQLKRFE HLLNGSNRKL DDFIEFPTYL NMKNYCSTKE KDKH SENGK VPDIIYELIG IVSHKGTVNE GHYIAFCKIS GGQWFKFNDS MVSSISQEEV LKEQAYLLFY TIRQVN

UniProtKB: Ubiquitin carboxyl-terminal hydrolase 8

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Macromolecule #9: Transcription and mRNA export factor SUS1

MacromoleculeName: Transcription and mRNA export factor SUS1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 11.094497 KDa
SequenceString:
MTMDTAQLKS QIQQYLVESG NYELISNELK ARLLQEGWVD KVKDLTKSEM NINESTNFTQ ILSTVEPKAL EMVSDSTRET VLKQIREFL EEIVDTQ

UniProtKB: Transcription and mRNA export factor SUS1

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Macromolecule #10: SAGA-associated factor 11

MacromoleculeName: SAGA-associated factor 11 / type: protein_or_peptide / ID: 10 / Details: This a zinc-finger containing protein. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 11.297625 KDa
SequenceString:
MTEETITIDS ISNGILNNLL TTLIQDIVAR ETTQQQLLKT RYPDLRSYYF DPNGSLDING LQKQQESSQY IHCENCGRDV SANRLAAHL QRCLSRGARR

UniProtKB: SAGA-associated factor 11

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Macromolecule #11: SAGA-associated factor 73

MacromoleculeName: SAGA-associated factor 73 / type: protein_or_peptide / ID: 11 / Details: This a zinc-finger containing protein. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 72.976688 KDa
SequenceString: MRSGDAEIKG IKPKVIEEYS LSQGSGPSND SWKSLMSSAK DTPLQYDHMN RESLKKYFNP NAQLIEDPLD KPIQYRVCEK CGKPLALTA IVDHLENHCA GASGKSSTDP RDESTRETIR NGVESTGRNN NDDDNSNDNN NDDDDDDDND DNEDDDDADD D DDNSNGAN ...String:
MRSGDAEIKG IKPKVIEEYS LSQGSGPSND SWKSLMSSAK DTPLQYDHMN RESLKKYFNP NAQLIEDPLD KPIQYRVCEK CGKPLALTA IVDHLENHCA GASGKSSTDP RDESTRETIR NGVESTGRNN NDDDNSNDNN NDDDDDDDND DNEDDDDADD D DDNSNGAN YKKNDSSFNP LKRSTSMESA NTPNMDTKRS KTGTPQTFSS SIKKQKKVKQ RNPTEKHLID FNKQCGVELP EG GYCARSL TCKSHSMGAK RAVSGRSKPY DVLLADYHRE HQTKIGAAAE KRAKQQELQK LQKQIQKEQK KHTQQQKQGQ RSK QRNVNG GKSAKNGGKS TVHNGNNINE IGHVNLTPEE ETTQVLNGVS RSFPLPLEST VLSSVRYRTK YFRMREMFAS SFSV KPGYT SPGYGAIHSR VGCLDLDRTT DYKFRVRTPQ PINHLTNQNL NPKQIQRLQQ QRALQAQLLS QQQQQQQQQQ QHHSP QAQA QASTQQPTQG MVPNHFPGGA TNSSFNANVS SKQIQQQQQQ QQHKSQDTGL TPLEIQSQQQ KLRQQQLQQQ KFEAAA SYL ANATKLMQES NQDSHLSGTH NNNSSKNGNN NLMTMKASIS SPNTSVNSIQ SPPSVNSVNG SGQGVSTGIN VSGNNGR IE VGIGNSVNPY NGRIN

UniProtKB: SAGA-associated factor 73

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Macromolecule #12: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #6: Widom601 DNA (145-MER)

MacromoleculeName: Widom601 DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.520383 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)

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Macromolecule #7: Widom601 DNA (145-MER)

MacromoleculeName: Widom601 DNA (145-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.99166 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DG) (DA)(DT)

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
1.0 mMC4H10O2S2Dithiothreitol

Details: Solution were made from stock solution
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 44.17 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 313986
Startup modelType of model: INSILICO MODEL
In silico model: cryoSPARC ab-initio reconstruction was use to generate the startup model.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 113856
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4zux


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 114.6 / Target criteria: Correlation coefficient
Output model

PDB-6t9l:
SAGA DUB module bound to a ubiqitinated nucleosome

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