[English] 日本語
Yorodumi
- EMDB-10438: SAGA bound to TBP - whole structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10438
TitleSAGA bound to TBP - whole structure
Map dataSAGA-TBP structure refined in CryoSparc
Sample
  • Complex: SAGA bound to TBP
    • Complex: TATA-box Binding Protein (TBP)
      • Protein or peptide: x 1 types
    • Complex: SAGA complex
      • Protein or peptide: x 12 types
KeywordsTranscriptional co-activator / Histone-acetylation / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase I transcription regulator complex / RITS complex assembly / regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / regulatory ncRNA-mediated heterochromatin formation / RNA polymerase III type 3 promoter sequence-specific DNA binding / SLIK (SAGA-like) complex / SAGA complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity ...RNA polymerase I transcription regulator complex / RITS complex assembly / regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / regulatory ncRNA-mediated heterochromatin formation / RNA polymerase III type 3 promoter sequence-specific DNA binding / SLIK (SAGA-like) complex / SAGA complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / transcription initiation at RNA polymerase I promoter / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / molecular adaptor activity / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcriptional activator Spt7 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / SAGA-associated factor 73 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. ...Transcriptional activator Spt7 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Transcription factor Spt20 / Spt20-like, SEP domain / Spt20, SEP domain / 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 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 / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / : / 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. / PIK-related kinase, FAT / FAT domain / FATC / 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 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
Subunit (60 kDa) of TFIID and SAGA complexes / Transcription initiation factor TFIID subunit 10 / TATA-binding protein, general transcription factor / Transcription-associated protein / Spt20-like SEP domain-containing protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act ...Subunit (60 kDa) of TFIID and SAGA complexes / Transcription initiation factor TFIID subunit 10 / TATA-binding protein, general transcription factor / Transcription-associated protein / Spt20-like SEP domain-containing protein / Subunit of SAGA histone acetyltransferase complex / Transcriptional coactivator HFI1/ADA1 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to act / Transcription initiation factor TFIID subunit 5 / Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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
DepositionOct 31, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseJan 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6tb4
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10438.png

Downloads & links

-
Map

FileDownload / File: emd_10438.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSAGA-TBP structure refined in CryoSparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 512 pix.
= 558.08 Å		1.09 Å/pix.
x 512 pix.
= 558.08 Å		1.09 Å/pix.
x 512 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-1.5468898 - 3.1253965
Average (Standard dev.)-0.00081884454 (±0.058872446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z512512512
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/NS512512512
D min/max/mean-1.5473.125-0.001

-
Supplemental data

-
Mask #1

Fileemd_10438_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half B map obtained with CryoSparc

Fileemd_10438_half_map_1.map
AnnotationHalf B map obtained with CryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_10438_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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 complex
      • Protein or peptide: Transcriptional coactivator HFI1/ADA1
      • Protein or peptide: SAGA-associated factor 73 (Sgf73)
      • 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 adapter 3 (Ada3)

+
Supramolecule #1: SAGA bound to TBP

SupramoleculeName: SAGA bound to TBP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 complex

SupramoleculeName: SAGA complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#13
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: 26.931299 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDSLKLPTTA AQAKAFTSSG SLSFPMNNDD MIKADPSQTE QHIIKQDIEP EIKDVVVSDD ANSSGIVPTL QNIVATVTLG CRLDLKTVA LHARNAEYNP KRFAAVIMRI REPKTTALIF ASGKMVVTGA KSEDDSKLAS RKYARIIQKI GFAAKFTDFK I QNIVGSCD ...String:
MDSLKLPTTA AQAKAFTSSG SLSFPMNNDD MIKADPSQTE QHIIKQDIEP EIKDVVVSDD ANSSGIVPTL QNIVATVTLG CRLDLKTVA LHARNAEYNP KRFAAVIMRI REPKTTALIF ASGKMVVTGA KSEDDSKLAS RKYARIIQKI GFAAKFTDFK I QNIVGSCD VKFPIRLEGL AFSHGTFSSY EPELFPGLIY RMVKPKIVLL IFVSGKIVLT GAKQREEIYQ AFEAIYPVLS EF RKM

+
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: SAGA-associated factor 73 (Sgf73)

MacromoleculeName: SAGA-associated factor 73 (Sgf73) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 79.995227 KDa
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

+
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: Subunit of the SAGA transcriptional regulatory complex, involved in proper assembly of the complex

+
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: Transcription initiation factor TFIID subunit 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: Transcription initiation factor TFIID subunit 5

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

+
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: Transcription initiation factor TFIID subunit 9

+
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 adapter 3 (Ada3)

MacromoleculeName: Transcriptional adapter 3 (Ada3) / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 6.485986 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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: OTHER
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: 0.0045000000000000005 µm / Calibrated defocus min: 0.0008 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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 354104
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-6tb4:
Structure of SAGA bound to TBP

+
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