[English] 日本語
Yorodumi
- EMDB-10446: SAGA-TBP filtered to show the position of the DUB domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10446
TitleSAGA-TBP filtered to show the position of the DUB domain
Map data
Sample
  • Complex: SAGA bound to TBP
    • Complex: TATA-box binding protein (TBP)
      • Protein or peptide: x 1 types
    • Complex: SAGA component
      • Protein or peptide: x 1 types
    • Complex: Polyubiquitin-B
      • Protein or peptide: x 1 types
    • Complex: SAGA complex
      • Protein or peptide: x 15 types
  • Ligand: x 1 types
KeywordsTranscriptional co-activator / Histone-acetylation / TRANSCRIPTION
Function / homology
Function and homology information


ADA complex / SAGA-type complex / DUBm complex / RITS complex assembly / pseudohyphal growth / positive regulation of DNA-templated transcription initiation / invasive growth in response to glucose limitation / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly ...ADA complex / SAGA-type complex / DUBm complex / RITS complex assembly / pseudohyphal growth / positive regulation of DNA-templated transcription initiation / invasive growth in response to glucose limitation / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / transcription export complex 2 / regulatory ncRNA-mediated heterochromatin formation / RNA polymerase I general transcription initiation factor binding / nuclear mRNA surveillance / SLIK (SAGA-like) complex / regulation of transcription by RNA polymerase III / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / SAGA complex / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / RNA Polymerase III Transcription Initiation From Type 2 Promoter / DNA binding, bending / RNA polymerase II transcribes snRNA genes / 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 / poly(A)+ mRNA export from nucleus / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / transcription factor TFIID complex / female gonad development / seminiferous tubule development / RNA Polymerase I Promoter Escape / NuA4 histone acetyltransferase complex / nucleolar large rRNA transcription by RNA polymerase I / histone acetyltransferase activity / Estrogen-dependent gene expression / male meiosis I / protein deubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / nuclear pore / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / energy homeostasis / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / 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 / TBP-class protein binding / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / regulation of neuron apoptotic process / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / Pexophagy / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation
Similarity search - Function
Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / Transcriptional activator Spt7 / SAGA complex, Sgf11 subunit / Sgf11 (transcriptional regulation protein) / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 ...Histone acetyltransferases subunit 3 / Histone acetyltransferases subunit 3 / Transcriptional activator Spt7 / SAGA complex, Sgf11 subunit / Sgf11 (transcriptional regulation protein) / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Spt20-like, SEP domain / Spt20, SEP domain / Transcriptional regulator of RNA polII, SAGA, subunit / SAGA-associated factor 73 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / LisH / 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 / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TAFII31 / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Lissencephaly type-1-like homology motif / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Ubiquitin specific protease (USP) domain signature 2. / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / : / PIK-related kinase, FAT / FAT domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / FATC / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / TBP domain superfamily / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Papain-like cysteine peptidase superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / WD domain, G-beta repeat / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature.
Similarity search - Domain/homology
TBP-associated factor 6 / Transcription initiation factor TFIID subunit 10 / Ubiquitin carboxyl-terminal hydrolase / Transcription-associated protein / Spt20-like SEP domain-containing protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation / TBP-associated factor 12 / Transcription and mRNA export factor SUS1 ...TBP-associated factor 6 / Transcription initiation factor TFIID subunit 10 / Ubiquitin carboxyl-terminal hydrolase / Transcription-associated protein / Spt20-like SEP domain-containing protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation / TBP-associated factor 12 / Transcription and mRNA export factor SUS1 / Transcriptional regulator involved in glucose repression of Gal4p-regulated genes / SAGA-associated factor 11 / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act / Subunit (90 kDa) of TFIID and SAGA complexes / SAGA complex subunit Spt7 / Ubiquitin B / Polyubiquitin-B / TATA-box-binding protein
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus) / Homo sapiens (human) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsPapai G / Frechard A
Funding support France, 3 items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0022-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02 France
CitationJournal: Nature / Year: 2020
Title: Structure of SAGA and mechanism of TBP deposition on gene promoters.
Authors: Gabor Papai / Alexandre Frechard / Olga Kolesnikova / Corinne Crucifix / Patrick Schultz / Adam Ben-Shem /
Abstract: SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to ...SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes. Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 Å resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression.
History
DepositionNov 1, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6tbm
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10446.png

Downloads & links

-
Map

FileDownload / File: emd_10446.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 256 pix.
= 558.08 Å		2.18 Å/pix.
x 256 pix.
= 558.08 Å		2.18 Å/pix.
x 256 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.023929587 - 0.031576734
Average (Standard dev.)0.000009551157 (±0.0011494906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0240.0320.000

-
Supplemental data

-
Sample components

+
Entire : SAGA bound to TBP

EntireName: SAGA bound to TBP
Components
  • Complex: SAGA bound to TBP
    • Complex: TATA-box binding protein (TBP)
      • Protein or peptide: TATA-box Binding Protein (TBP)
    • Complex: SAGA component
      • Protein or peptide: Subunit of SAGA histone acetyltransferase complex
    • Complex: Polyubiquitin-B
      • Protein or peptide: Polyubiquitin-B
    • Complex: SAGA complex
      • Protein or peptide: Transcriptional coactivator HFI1/ADA1
      • Protein or peptide: Spt20
      • Protein or peptide: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act
      • Protein or peptide: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
      • Protein or peptide: Transcription initiation factor TFIID subunit 10
      • Protein or peptide: Subunit (61/68 kDa) of TFIID and SAGA complexes
      • Protein or peptide: Subunit (90 kDa) of TFIID and SAGA complexes
      • Protein or peptide: Subunit (60 kDa) of TFIID and SAGA complexes
      • Protein or peptide: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
      • Protein or peptide: Transcription-associated protein
      • Protein or peptide: Transcriptional regulator involved in glucose repression of Gal4p-regulated genes
      • Protein or peptide: Spt8
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase
      • Protein or peptide: SAGA-associated factor 11
      • Protein or peptide: Transcription and mRNA export factor SUS1
  • Ligand: water

+
Supramolecule #1: SAGA bound to TBP

SupramoleculeName: SAGA bound to TBP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Molecular weightTheoretical: 1.6 MDa

+
Supramolecule #2: TATA-box binding protein (TBP)

SupramoleculeName: TATA-box binding protein (TBP) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Komagataella phaffii GS115 (fungus)

+
Supramolecule #3: SAGA component

SupramoleculeName: SAGA component / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Komagataella phaffii GS115 (fungus)

+
Supramolecule #4: Polyubiquitin-B

SupramoleculeName: Polyubiquitin-B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #15
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #5: SAGA complex

SupramoleculeName: SAGA complex / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2, #4-#14, #16-#18
Source (natural)Organism: Komagataella phaffii GS115 (fungus)

+
Macromolecule #1: TATA-box Binding Protein (TBP)

MacromoleculeName: TATA-box Binding Protein (TBP) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Molecular weightTheoretical: 27.042275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF ...String:
MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF PIRLEGLAFS HGTFSSYEPE LFPGLIYRMV KPKIVLLIFV SGKIVLTGAK QREEIYQAFE AIYPVLSEFR KM

+
Macromolecule #2: Transcriptional coactivator HFI1/ADA1

MacromoleculeName: Transcriptional coactivator HFI1/ADA1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 49.888273 KDa
SequenceString: MASTELVAST PMPSRNGQGS HQKLNGGNVN SATNTPTVAS TPVNQPRKLP SENFSGLGGA IRIEIEPLVV DFQRRLGKNW GRYQIAVSL FLVGKLSRRE LVDELDDILD RNTVKMHNQL LLGNLANSLK ESAGDRVGSG GFGGSMFNKR VKDSRKSSQY E RLKRDILA ...String:
MASTELVAST PMPSRNGQGS HQKLNGGNVN SATNTPTVAS TPVNQPRKLP SENFSGLGGA IRIEIEPLVV DFQRRLGKNW GRYQIAVSL FLVGKLSRRE LVDELDDILD RNTVKMHNQL LLGNLANSLK ESAGDRVGSG GFGGSMFNKR VKDSRKSSQY E RLKRDILA LPVRERRRIK AITRESGKKG MVNSVITQTR QALIPKVPVV TRPTNVPGNS VQWAQDVIHG FQALLASEIY EL PEMDNLR TRMTGISREH GLIGPVDDSV IEIMLIGLEQ HLKGIVEAAI DIVKYRRTKY TNNSVVDTLQ KEQTNTSDTS SSK VSRKRD RHTLTIEDMY DTLEQYPYLV EPGGTLLRLQ SVMLHDEDEL SDDEILKHIL KPRTSDSTDR KPKQLQENGT ADSL SKVTK SITNGANASG DAVPNGKAEH IQNTMGTKEE LNWFIYDILS NNE

UniProtKB: Transcriptional coactivator HFI1/ADA1

+
Macromolecule #3: Subunit of SAGA histone acetyltransferase complex

MacromoleculeName: Subunit of SAGA histone acetyltransferase complex / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 79.995227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQNPERPVVW KELGQYLDTL QPIHQEKPSS LPDLPSPSYK DSLSNPLRYR ICNNCDRPIL QSCLSKHIKI CNQIVKVEKL EEDDKPMNM VRKRKNQVLE ESKESTPVTN TNSTNSSNAI NSTTSKKTKK VKLPKEKKPK KERVKSTAKP KGPVDVERQC G VPLPNGGY ...String:
MQNPERPVVW KELGQYLDTL QPIHQEKPSS LPDLPSPSYK DSLSNPLRYR ICNNCDRPIL QSCLSKHIKI CNQIVKVEKL EEDDKPMNM VRKRKNQVLE ESKESTPVTN TNSTNSSNAI NSTTSKKTKK VKLPKEKKPK KERVKSTAKP KGPVDVERQC G VPLPNGGY CARSLTCKTH SMGAKRAVPG RSAPYDQLLV AYQRKNQAKF AANAAAAHAA RDDLIHGSQI PIDEDDEAHQ VL DGVAKSY PLPLERKVIM PARSRSSFLR MREMFAGAIL PRVPTNPFGN LYSRTAVIDV DRAGDYYFSV RASPRMPNQQ QNK TQKNPQ PPRPQVQQQQ QAQKSQQSPP QAQQQISQSA GQQTSQTVQR LVQQQQRLQQ QRQQTQIQQQ QQHQQQQQQQ QHQQ QQQQQ QQQQQQQTHM LQQQQQQQQQ QQMLLLQQQQ QQQAQQQQSP PITHQSPIPD NRPSNQLPQQ YSQMTPQQLQ LQQQL QLQQ KQKEQFRLQQ QQHLRNL(UNK)MR (UNK)TPQQQQQFA NLTPEKRAQF QRMQLVQLQQ QIKNQAIQNQ MQQQQQQP S HVQSQAQTQF QQAQLKAQSR AQVLQAAQRQ MQNSPTSPVT SMSSPLAIPS NLANQGPNQT SQLPNEQLSN PLMGNQFQG QFNQYQPNYR ENLEGGGGSM DEKTTGWRGG HVVEGLAGEL EQLRARLEHH PQGQREPGGS HHHHHH

UniProtKB: Subunit of SAGA histone acetyltransferase complex

+
Macromolecule #4: Spt20

MacromoleculeName: Spt20 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 59.530578 KDa
SequenceString: MSQIQSSQVG AKNMQTAQPQ AQQRPINGSV TLSNGQRINP QNLTPQQQRL LQQKVLHQKL KNYKFAETSE EILHKYEKFP PSLTFHIHE NHYRFGDQDG VIPKNSSVIK AFLEYVAREE IPPALIEVTK DAGVQLYEGC IILRIYDHRH LVAHINDAKD S QHVSSESS ...String:
MSQIQSSQVG AKNMQTAQPQ AQQRPINGSV TLSNGQRINP QNLTPQQQRL LQQKVLHQKL KNYKFAETSE EILHKYEKFP PSLTFHIHE NHYRFGDQDG VIPKNSSVIK AFLEYVAREE IPPALIEVTK DAGVQLYEGC IILRIYDHRH LVAHINDAKD S QHVSSESS ANNTNNEKKE PSKVPKTYTT ILRPTQLSLY ADLLYQTDYL QVRFTDSLSL NIETEILTAS KRNLDLSVPL NP HRATANL KPEVKYPYYD PETDTVVHEH RPDARGNMVN ADTVDYRKLH EDMAQHGSDY ERLMLLLSDR FDDDSQTQGS SVT SSQFMR LRFVEAWRKK EERLQESGGS SQRQRPLQPG QIPGMLSSFS SNTGNMNTML DNLTPQQKAA IQQRMIQQGR AQPQ QQQPD QEQLQEQQQQ QPQQAMSQQR QQQLQQLYQR QQQHNQHHQQ NQDELSSLDD KKIKKPPAKK QKKMTKKEMT TLHQN VAGK TIPSAESTPP TTAANKKRGT YKKKNKYILI IND

UniProtKB: Spt20-like SEP domain-containing protein

+
Macromolecule #5: Subunit of the SAGA and SAGA-like transcriptional regulatory comp...

MacromoleculeName: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 39.030105 KDa
SequenceString: MTDAKDKDHK YRYRMEIQQM MFVSGETNDP PVETTSLIED IVRSQVVEIV LHSSQTALSR GTKSIVPEDV IFLIRHDKAK VNRLRTYLS WKDVRKNAKD QQSGDLADIG GDDLLDNSTS QVAASGAPGA PGSSSSTSMD SKMLSKYKKS KIRLPWELQF V FTEQPLDT ...String:
MTDAKDKDHK YRYRMEIQQM MFVSGETNDP PVETTSLIED IVRSQVVEIV LHSSQTALSR GTKSIVPEDV IFLIRHDKAK VNRLRTYLS WKDVRKNAKD QQSGDLADIG GDDLLDNSTS QVAASGAPGA PGSSSSTSMD SKMLSKYKKS KIRLPWELQF V FTEQPLDT NEDDAEDEDE RAATLASLKR LKTNDERTKN MTKEEYVHWS ECRQASFTFR KAKRFREWCG LSHLAESRPS DD VIDILGF LTFEMVCSIT EEALIVKMLE EQNGDLASST TTIQKLQESH RKRKHLFDGP DKDVRPITSG HVLEAWRRLQ KRN VEKKAI RNFQGGKLRS RVQLI

UniProtKB: Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act

+
Macromolecule #6: Subunit of the SAGA transcriptional regulatory complex, involved ...

MacromoleculeName: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 136.768828 KDa
SequenceString: MANERALQYF VTSDNQRLYD LAAKLFSLGF FNCYFTPQQF QLLSVILDNG KLRIEEDGFV STVWDEFIKG RLVLQFSKGD YEKESTKHT VDNVKGTDDK TGIEVSKENG HSSDPPSADH DITESDNVGR EETLDDQFSE LYLKDGVSTS QFMCAKLRYL L FEQAIDYL ...String:
MANERALQYF VTSDNQRLYD LAAKLFSLGF FNCYFTPQQF QLLSVILDNG KLRIEEDGFV STVWDEFIKG RLVLQFSKGD YEKESTKHT VDNVKGTDDK TGIEVSKENG HSSDPPSADH DITESDNVGR EETLDDQFSE LYLKDGVSTS QFMCAKLRYL L FEQAIDYL YTNSSMNGDA EEYSLLQNVD DMNEEKEETA KPATPQNVRE IDNDYDDDED EDEEDEEIKE ASSKNPFKTE DN EPLTNER QPTNNVFIRL CSDEKSLSKS LTLNLLTSMV TSKPEYPVEQ LKGSEVIGTS HPLLGTASAI ESKLEKRNEA RLI KNFSKI YHQFDKDERN FLKRRKLEIS NKQFLDQDNN DPKDRPSSNS TSDEESNSNN LEKTSQPSSV NKLMQLGGAA NLSL KNLLS KVEENREKLN LSDLDLRSLI MDVRKNRSKW ASDDKIGQEE LYEACEKVVL ELRGYTEHST AFLNRVSKRE APNYY QIIK KPMDLNTVMK KLKSFQYKSK QEFVDDLMLI WKNCLTYNSD PSHFIRVHAV AMQKKTLSLI PLIPDIVIRD RSELEK DEV ENVVETPQSS SIGTPMTTRV AGGKGPKKGR THREPPTRPE TPDGIAGEDS SQVSKAEQDS PAKALEVTEN DSTKEKE KD LSDVPTQEQK NDKTEKDDDY QEAVEDEEED DDDNTNLEED STEDEDDLEV QTWNSLTSNV RYKICEKRRN LFKENKIQ P NEEAIFRDTY QMENFMHYLG DDVRIVLNTP MSRYQYYDGN EDPYLIEYDI SGGIPGLKYS GVSPDEGDLE DNMLVDQLM KGESSIRESG FARKPTGMNK KFNEIIHLMQ QIRRICFKIS LIRQMQTQQF LHHTQMKPPD INEIQDIDID QLSNLPNRDK LDSDVSYNS LKRSISKILM ANGFESTAPF CSDVITQIAE NYFGNLVKTL KNHIESKSIN KVMGDAKFQK VSNKDILLLS L LENGVESP DALYEYYNEN IVKQISKLEG LKSRLSSFLA ELLRPGLQDL NERQFNDNSD EFLTGNFSSE IGDDFFGFRE LG LEKEFGL LTSTVPLHLL HSRLNSSIFN SNHEVSQLKF DDIQAEEKEQ LYKREIPQHI KLIQPFLYNI AEKSKTIHYK QLK KLNELQ KMPENDDDIL LIEDEDLPLK QRNTRPRVPP TGKIPNVKKK AVNGAYFLDP AIFSSNNQVK VEGDT

UniProtKB: SAGA complex subunit Spt7

+
Macromolecule #7: Transcription initiation factor TFIID subunit 10

MacromoleculeName: Transcription initiation factor TFIID subunit 10 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 23.879145 KDa
SequenceString: MSTEKLFEDL DEDSLMQDVE GGVEGSMTIE EEPEPNDEKE APHISMPSLP EYTRKDKTLE EILEMMEDEE FTPIIPDAVT DYYLAKNGF ETSDIKIKRI LALATQKFIS DIAQDAYEYS RIRSSSSVYT SANPQARARQ LVAGQQQQQQ QQPQQQQQQQ P QTGASQPA ...String:
MSTEKLFEDL DEDSLMQDVE GGVEGSMTIE EEPEPNDEKE APHISMPSLP EYTRKDKTLE EILEMMEDEE FTPIIPDAVT DYYLAKNGF ETSDIKIKRI LALATQKFIS DIAQDAYEYS RIRSSSSVYT SANPQARARQ LVAGQQQQQQ QQPQQQQQQQ P QTGASQPA PTVGGSGGGG GGGGGTSTGT NNKVVLTMDD LRSALGEYGI NVKRPNFYR

UniProtKB: Transcription initiation factor TFIID subunit 10

+
Macromolecule #8: Subunit (61/68 kDa) of TFIID and SAGA complexes

MacromoleculeName: Subunit (61/68 kDa) of TFIID and SAGA complexes / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 66.690133 KDa
SequenceString: MNQPPNQPQD NDSQVSSSGM QGGNSMNYSS SAPVNGAGQG PQPQQNSQGQ NGKKPVGMQQ AQIQLLARRY QLEMQKAHQL GPQTPQGAE HLQTATKIKH VLLSYQQQRQ RQQGQVQGQG LSQPQGQNQA QGRVQQQTQG LSPDPGSHQG SPQFQQPHQV M MGSAQTAG ...String:
MNQPPNQPQD NDSQVSSSGM QGGNSMNYSS SAPVNGAGQG PQPQQNSQGQ NGKKPVGMQQ AQIQLLARRY QLEMQKAHQL GPQTPQGAE HLQTATKIKH VLLSYQQQRQ RQQGQVQGQG LSQPQGQNQA QGRVQQQTQG LSPDPGSHQG SPQFQQPHQV M MGSAQTAG TSIANPQAQS NISSQVSQMA AAKVNSASPP IPPKTVGTPT GTPVGTQPRG QVTIQQFQQV KSILEEFEKK LR TIEAAKR DQNLPEETLQ KLLRQEAILK QRYAQTKATA YQMSQHLQRQ QQALRAASAE SAEVYVTGSA SSPNMNVYNQ QIL TQQPQQ QLQQQQLHQP QPQQPQPARQ SPHLLIHQQQ QQQQQQQQQQ QQQQQHPVTH RPSNVSQTMP QPSQPLQSST PSSA VGRNQ SPGATPVTSV NAAAKPSPGT SSTSTLINQH ILKPAPPPTE IPARLQVKPP QPAAMKIPNR PTLLGGSAIS QPSLT TPVS IRPPPLEMEG DHVLQKRKLK ELLRNVGADE GDGETVIDGD VEELLLDLAD EFVTSVTSFA CRLAKHRKVD NIDMRD VQL HLERNWNIRV PGYASDEIRS VRKFQPTAGY NQKVQGVAIS KSVNKN

UniProtKB: TBP-associated factor 12

+
Macromolecule #9: Subunit (90 kDa) of TFIID and SAGA complexes

MacromoleculeName: Subunit (90 kDa) of TFIID and SAGA complexes / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 80.933008 KDa
SequenceString: MKQEPGDSSD KSAPSGSITP QPKPPQQANV SNQQPQKPQQ FSAADLNRIV LEYLNKKGYH KTESMLRMES SHIPAPPTNI PTPQTTNIS RPTAPGRAPE YSDDPATIKR GYSILKSWCE SSLDFYRPEL EKFLYPVFVH CYLDLIARGY PSHAREFYDK F SKDHSVLH ...String:
MKQEPGDSSD KSAPSGSITP QPKPPQQANV SNQQPQKPQQ FSAADLNRIV LEYLNKKGYH KTESMLRMES SHIPAPPTNI PTPQTTNIS RPTAPGRAPE YSDDPATIKR GYSILKSWCE SSLDFYRPEL EKFLYPVFVH CYLDLIARGY PSHAREFYDK F SKDHSVLH EYEISKLGGI SLKEHLQEND VAKIFRSHKF KVLIGRTTFN LLLYFLNEND AVGGGVVLRL INQYIEPVIT TE AIAVERE GELNLSEGIV ELHTLNNTSI GGEQREISSV DAFNKKPVKL GKLQVDPEYS KELEAELKLK DEHEQAAQKK VST TLLEEY RENFKVDPSD ENNPSKDTLP LPLKSAQDLR NDIAMIQDSR AKIKLSAAQA SLPSVCMYTF HNTNNDLTCL KFND DSTMV ASGFQDSFIK LWSIDGSPLR SLLKNDPYNQ QNNDGVAVKG SRRLVGHSGA VYGVDFSPDN RYLISCSEDK TVRLW SLDT YTCLVSYKGH SSSVWDVKFS PMGHYFATAS HDQTARLWSC DHIYPLRIFA GHLNDVDCVE FHPNSTYLFT GSSDKT ARM WDIARGECVR VFMGHSGAIN CLAVSPDGRW LASAGEDSVV CLWDISTGRR IKAMRGHGRS SIYSLAFSRE GTVLVST GA DNSVRVWDVK KNTNSPSAQP EPINDVTAQG IQKKTEDLRR RKEIVATNDH MSVYFTKKTP VYTVHFTRRN LCLAGGVF G G

UniProtKB: Subunit (90 kDa) of TFIID and SAGA complexes

+
Macromolecule #10: Subunit (60 kDa) of TFIID and SAGA complexes

MacromoleculeName: Subunit (60 kDa) of TFIID and SAGA complexes / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 54.888445 KDa
SequenceString: MSKNSQRSSI PTSHTLWSPS DTVKDAAESL GIFNLNEEAA KNLAMDIEYR IHEILDQASK FMRHGKRRTL HTSDIDRALK VLNLEPLYG YDVSRPLVFK EALVGAGQNL YYVDDDEVDF EKLINEPLPK VPRFSTFTAH WLAIEGVQPA IPQNPSPNDI K NILPINRG ...String:
MSKNSQRSSI PTSHTLWSPS DTVKDAAESL GIFNLNEEAA KNLAMDIEYR IHEILDQASK FMRHGKRRTL HTSDIDRALK VLNLEPLYG YDVSRPLVFK EALVGAGQNL YYVDDDEVDF EKLINEPLPK VPRFSTFTAH WLAIEGVQPA IPQNPSPNDI K NILPINRG SMENMFSLIN DEVKEDTNEE FTSTGPSVSS NISNQKQGLE VKPLVKHVLS RELQLYFDKI VEVLLNQEET KE AELLRNS ALQSVRADPG LHQLVPYFIQ FISETITKNL KNISLLSTML ELIYSLLMNE SLFLEPYVHA IIPCILTLLL AKK IGNVDD ELQKQQQLAL RELSASLLER VIEDFGSSYS TLKPRITRTL LRAFVSVNNT TPGTQYGALL GLRGLGSEVI RIVV LGNVI NWSSTFLEKL QQEDQVFLID TLIETLRVLT KEGKLVKDMK TENGIDNERL KQRVGDLIAD RIQACDDAQD IYWGI FFGE V

UniProtKB: TBP-associated factor 6

+
Macromolecule #11: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA pol...

MacromoleculeName: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 17.303576 KDa
SequenceString:
MTNEQAAIPR DVRLLHLIFA TQNIYSYQDH VPLQLMDFAY RYTTGTLQDA TIYSDHAHAS GSHISNAGNA GTNAQLTTED IRLAIAART NYQFKPVPPK ELLLELAAER NKKPLPAVIP TWGIRLPPEK YCLTGKDWVL EDEEEAVSYK KRKT

UniProtKB: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation

+
Macromolecule #12: Transcription-associated protein

MacromoleculeName: Transcription-associated protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 438.055344 KDa
SequenceString: MLHVVQLDDF ATRLKAAEDY QSKHSVLSEI CDSLETFNAA QDYEYFLKSL IPLFIDVLKE VPVSFVANSP ENKLRNITLE ILHRIPAND ALQAYSNEIV DTLMDLLKVE NELNGILCMK AITTLHKTFK ASLQEKVHPF IDIVIEIYSN IPQVVEEQFN G NQIDSKEN ...String:
MLHVVQLDDF ATRLKAAEDY QSKHSVLSEI CDSLETFNAA QDYEYFLKSL IPLFIDVLKE VPVSFVANSP ENKLRNITLE ILHRIPAND ALQAYSNEIV DTLMDLLKVE NELNGILCMK AITTLHKTFK ASLQEKVHPF IDIVIEIYSN IPQVVEEQFN G NQIDSKEN VDSTSRPNSP SFSSQSDDSK QLAQAMFSFK TLAESPITMV SLYSSYKELA ASSLGNFIPH VMKVLSLEVA KQ AEARKAA EEKGIILVNV CKEITNRANY GEFIIGQVKA ASFLAYLFIR RQAQTFLEPY QQAIPDIIIR LLQDCPSELS AAR KELLHA TRHILSTDFR KMFIPKIDLL FDLRVLIGEG FTAYETLRPL AYSTVADFIH NVRDHLTPAQ LWKSVSIYCK NLQD DSLAL TVQIMSAKLL LNLIEKIMRS ESKTESRQLL MVIIDAYTKR FKMLNSRYNG IMKQHATYEK EKQEKQNQER LLTNK LDGT TPSPSDDKKV ELIDEDQDVK MEDPTPEISD QETIKGDNDA STEPQDSEQQ LADFMSLQEY LPIQVSVPPE IDLLKD SRY LFKTLMTFLK TIMIGLKNSN PPSSQNHFNA QNWNETARGF SNEDINILKS LFRECILALR FFSTSKTSLP ASSMKQS FD ITGPNLPITS TKEEKDLMEI FATMFIHIDP ASFNEIVREE LPFMYKQMLD FASLLHIPQF FLASVITSSS FSGILITF L KSKLVDLGEV NIIKSNILIR LFKLCFMSVS LFPAANESVI LPHLNELILK SLKLSTTAKE PLVYFYLIRT LFRSIGGGR FENLYKEIMP LLQVLLESLS KLIHEARRPQ ERDIYVELCL TVPVRLSVLV PHLSYLMKPL VYALNGSQES VSQGLRTLEL CVDNLTAEY FDPIIEPVID DVMEALSKHL KPLPYYHQHS HTTLRILGKL GGRNRTFIKP VDNLKTDSEL FQNVEAMFKI H GLPNEVPL SITPGLSAAF SLLTDPRPRI HYRINSFKYI SGIFQLFLGA TQLPDDYANR LKESMDIILE DTIAPDEPLN KL HHFPVKD IAKYDSQMEL LVKLLESIFY AVSLQEVREE SKALIRGTCN HFILLYFNKM VIDKRKFVRK FSVDNHEGNL FLN ENCIFD AIIYALSSDN SAVRSMGLES VQLIYDSCVE LFGNIDCALK FAPLNVMCSK FIHCCFEEPY HKKLAGCIGL EMML NSLDI PMKYFNARQL EIIRALFYVL RDTAPELPCE VTNTAKRLIL NSLKEWNKEL TRNDVFSSVF QNLVSSLIVD LPNAN EIVR ATAQEALRTL SETTQVPIAT MISPCKHILL APIFGKPLRA LPFQMQIGNI DAITFCMGLE NSFLEYNEEL NRLVQE ALA LVDAEDESLV SAHRISEHKT SEQLVRLRVV CIQLLSLAIT KPEFAAAQQR SNIRVKILVV FFKSLCGRSI EIIRAAH GG LKAVIDLKMK LPKELLQNGL RPMLMNLSDH KKLTVASLEA LSGLLKLFIS YFKVGIGSKL LDHLLAWAQP RTLQQLGS Q DLENNSTVQI IVAILDVFHL LPPTAHKFMN DLMNALLYLE NNLHRCQYSP FREPLAKFLD RFPDESFEYF FNEFSKREI TTRFVYFVGL DSCSSLRAKV LESLPRVRGL LHQEGSAEEK CVRFSNLVDL CESLAASDKE WIKDKEELLG ELLDAGSVCL TLKRSSNVV SPLYFQVDQG FETLQLLYIE YFKSQPLGHE KVFNFIDKIS KEGLPFVLEF DDFIFNEVVK CQDIPTVQQT L DTIIRMTP QVSSLDARVY LYKRIFLPIC IYESEMHGDL SRLSQTENNE LPAWLKSFDS DVWKATGPLV DDYTSTLEDR YR LELMQLT ALLIKGAPTA LTDMRKDIIK FSWNYIKLDD NTSKQAAYVV TAYFISRFDT PSELTTRIFV ALLRCHQIDT RYL VKQALE LLAPVLSERT NSELDWLKWP RRVLSEDGFN ITQVANIYQL IVKFPDLFYP ARDHFIPNII TAMGKLTVMS NTSL ENQQL AIDLAELILK WETKLPKSEK LGSAEETEKE KSVSEDKMDI DVKEETKEDI AERPKAEDQI GGDDSDSSNI LTSED YEVS FAQREACVTF LIRYICISTQ RPSENELGKR ALNILYELLG PKYWSEVTVK LQFFERFLMS SDLNQPSLLG YCLNAL EVL AVALKWKPTT WIIENVSYLQ KLLEKCLRSD NQDIQEILQK VLGIILEAIN KETQGSEEDE PEEVTNFISL IVNIIGE DL SNMTSVAAGV SLCWTLSLYR PNALDSLLPS IMRTFNKLCR DHIAISLQGN QPQSGDFANI EFEAKVTTNL LEKILNLC A ARISSLDDQR RVFLSLLAQL IDRSVDKDML LKVINIVTEW IFKTDFYPTT KEKAGILGKM MIFDLRGEPE LSKKFNQVI VDIFESKELA HTELTARMET AFLFGTRLSD VSIRKKLMSI LSDSLELDID KRLFYIIKDQ NWEYLSDYPW LNQALQLLYG SFHLDSPIR LSPEENTLSP LQSITEGLAR EKSPVEKAPQ NIIDFVAKHN EFLDSVRSLT AGDILNPLID ISYQSAETIH N AWVVVFPV AYSAIESRYE LEFTRALVKL LFKDYHIRQQ DARPNVIKSL LDGVGKCPGL HLPPHLVKYL GSNYNAWYGA IK LLEELSE GQGIDNQKIS DANQDALLEV YMSLQEDDMF YGTWRRRAKY FETNAALSYE QIGIWDKALQ LYEAAQIKAR SGV FPFGES EYSLWEDHWI YCAEKLQHWE ILTELAKHEG FTDLLLECGW RGADWIADRE PLEQSVKTVM DIPTPRRQIF QTFL ALQGF SQQKDTLQDV SRLCDEGIQL TLRKWNALPQ RVTRAHIGLL HTFQQYVELM EASQVYSSLV TTNAQNLDVK SQELK RVLQ AWRERLPNVW DDINIWNDLV TWRQHVFGVI NRVYMPFVPV LQQSNGTNNG NSYAYRGYHE MAWVINRFAH VARKHE MPE VCINQLTKIY TLPNIEIQEA FLKLREQAKC HYQNSSELNT GLDVISNTNL VYFATQQKAE FFTLKGMFLA KLNAKDE AN QAFATAVQID LNLPKAWAEW GFFNDRRFKE NPEEIFHAKN AISCYLQAAG LYKDGKTRKL LCRILWLISL DDAAGSLA K TFEDHHGESP VWYWITFVPQ LLTSLSHKEA KIVRHILIQI AKSYPQSLHF QLRTTKEDYQ AIQRQAMAVN RAEEQSSNK QDTADSVLKN TNTPQPQTRT ETSGTTAESD KKPSIPPKEE QGSPQPSRPA TTQASPQAQS QENGESSQKH PPEIPTTDSR QPWQDVEEI MGILKTAYPL LALSLESLVD QLNQRFKCNA DEDAYRLVIV LYNDGVQQMN RVANPREEVK LPAATEASIS R FADSVLPK NIREVFEQDI IACNPNLETY ISKLRKWRDC LEEKLDRSYG KADLERVSLH LSLFHHQKFE DIEIPGQYLL HK DNNNHFI KIERFLPTLD LVRGSNGCYK RMTIRGNDGS LHPFAVQFPA ARHCRREERI FQLFRIFDDA LSRKVQSRRR NIS LTLPIA VPLSPHIRIL NDDKRYTTLM GIYEEFCRRK GQSRDEPFAY TIQKLRAAFD PRLPKPDIVS VRAEVLASIQ STLV PSTLL KDYYTEKFSN YENYWLFRKQ FTAQYASFIF MTYIMCINSR QPQKIHINEG SGNIWTSEML PTKVATGKTH STAYN NSTL DPAVKAGAPI FYNTESVPFR LTPNIQKFIG EAGLEGILSV YILVIANSLS DSEFDMEQYL SLFVRDEVIS WFAQQH RAS AQTNQLREIV RVNVELLTKR VLQLNHIPNS QNVATQFVLN LISQAVNPRN LAYTDSAWMA YL

UniProtKB: Transcription-associated protein

+
Macromolecule #13: Transcriptional regulator involved in glucose repression of Gal4p...

MacromoleculeName: Transcriptional regulator involved in glucose repression of Gal4p-regulated genes
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 81.864305 KDa
SequenceString: MAARSSTRRG GQPPGVAKSL GSNKSSPVKK GLGAGKGKPK VDYPKQNPSS TLHDILSELN LSYDSNLGLL QGDGIAFPPS VSVLNNVKG LFEQLIEELQ YVSNYDDNLL KIIDNKLKEI EHKPSTGEVK EEEIDGTESE QPARKRQKVQ STDRIEIPDT K PQGLPLKE ...String:
MAARSSTRRG GQPPGVAKSL GSNKSSPVKK GLGAGKGKPK VDYPKQNPSS TLHDILSELN LSYDSNLGLL QGDGIAFPPS VSVLNNVKG LFEQLIEELQ YVSNYDDNLL KIIDNKLKEI EHKPSTGEVK EEEIDGTESE QPARKRQKVQ STDRIEIPDT K PQGLPLKE SSSQKVDSKT SVKDEAKEDE IGDDNDDDDE DDAMEEDEAG DDDEDEEEAE IEGEAGIGGE PGAEAAVEAD DD EEDEEVE EEEAASEAKP VVKEGFEQEG HYTRENDTRV KNPKSEFVTS QTLPVAAVEL GLYDENGLEQ TGEDYYKRKY GVA SYPTSD LKEFLPGELP DEDFTKSKPP SQVQFSTFQS YLEPYFRPFT EEDIKFLKKQ YNLPQNLPKN YDPNVTPFVI PKFG AHYRD TWYEEDINTG MIKKKPNDVD PRLADQKMRQ DALIPKGSGA SLTDDVLETE KVSCGPLASR LLSALLKNGD DTEDG EPVD NDDNNNVSSA IGNEGWTPSV ETSDYETLDQ RLRRELKYIG VFMNVEQTLK REGHADELVN SVGVTSGNGE FEEDWL NSR EDDEISAEMR SLQRELRRLT RKNVRRKEKL IPIVEEQLAW QEYQSILEDL DKQVDQAYLR RIRVPRKNKR KNESQSS GQ QTQQQQQQQQ QQQQQDQQQT GFKALLDKRT RWIEKIGPLF KPPHLMRRPP SESVFKDVDL ENDDEELEED DEMKVDID L R

UniProtKB: Transcriptional regulator involved in glucose repression of Gal4p-regulated genes

+
Macromolecule #14: Spt8

MacromoleculeName: Spt8 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 34.059902 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

+
Macromolecule #15: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.560831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG(GLZ)

UniProtKB: Ubiquitin B

+
Macromolecule #16: Ubiquitin carboxyl-terminal hydrolase

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 56.745879 KDa
SequenceString: MTSTVKKTLE EAKFSPPVFD SCPHLKQILT SNAKDTVYRN YGLAVNVALA LKLRNGNIPL YKTSDGSKVE YKKLARLRNK AVRCRECLE SLSCTYFCLQ CSHVGCWKNG HASAHTKSTG HVFGIDSQTG YIFCFRCGDY VGDQRLEFIR QSKQGERTEP I MNNLGTET ...String:
MTSTVKKTLE EAKFSPPVFD SCPHLKQILT SNAKDTVYRN YGLAVNVALA LKLRNGNIPL YKTSDGSKVE YKKLARLRNK AVRCRECLE SLSCTYFCLQ CSHVGCWKNG HASAHTKSTG HVFGIDSQTG YIFCFRCGDY VGDQRLEFIR QSKQGERTEP I MNNLGTET IIDGSRPPSL KASTGLRGFI NMGATCFMSS IVQTIVHNPF VRDYFLSGYH AKCTKKMDTC ITCCIDEIFK VF YGTDETK GYGPTALLTA AWRVKNSLAG YSEQDAHEFW QFLLDEIHKS DTELHPELDD TSTCRCITHK TFAGQLQSTV TCE KCLHSK NTVDPMLDLS LEIAKISKDK VTLNDCLDLF TSKEKLDSMT ICSHCKKETT RTKQLLVRKL PPILAFQLKR FEHS ASSST KIETHVGFPL FLDMEPYTVS ETLNSNEQGR ASWGLMTYQL FAIVIHIGSV NTGHYICIIK NRDGNWFKFD DSRIT LVSQ DYVSKSNAYL LYYILCQA

UniProtKB: Ubiquitin carboxyl-terminal hydrolase

+
Macromolecule #17: SAGA-associated factor 11

MacromoleculeName: SAGA-associated factor 11 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 13.977742 KDa
SequenceString:
MSSEVMQETI WDCLMSNILR QIVINNILQE QALRSSIKAI SNDDQISLKE INAQRLKFVK DDKDIFNHIN GKRSENKYNG TGADASNGT TDTEYFTCLN CDRKIAGNRF ASHVDRCLGG RTRK

UniProtKB: SAGA-associated factor 11

+
Macromolecule #18: Transcription and mRNA export factor SUS1

MacromoleculeName: Transcription and mRNA export factor SUS1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 11.126675 KDa
SequenceString:
MTNSDVQHLK QQIQDVLVES GKYDELSNFL RSKLYQVGWT DEINRLTQSI VTNEAKPTFS NVIERIEPKA MDIVPEHIKT EILAKIEEF LKDVVPK

UniProtKB: Transcription and mRNA export factor SUS1

+
Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 91 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 52.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.5 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1068534
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 354104
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-6tbm:
Structure of SAGA bound to TBP, including Spt8 and DUB

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more