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- EMDB-0251: Molecular structure of promoter-bound yeast TFIID -

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Basic information

Entry
Database: EMDB / ID: EMD-0251
TitleMolecular structure of promoter-bound yeast TFIID
Map dataKomagataella phaffii TFIID
Sample
  • Complex: Transcription Factor IID
    • Protein or peptide: Taf2
    • 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: Taf8
    • Protein or peptide: Histone-fold
    • Protein or peptide: Histone-fold
    • Protein or peptide: Subunit (61/68 kDa) of TFIID and SAGA complexes
    • Protein or peptide: TFIID subunit (48 kDa)
KeywordsComplex / Transcription initiation / TRANSCRIPTION
Function / homology
Function and homology information


regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / chromatin organization ...regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / transcription cis-regulatory region binding / protein heterodimerization activity / chromatin binding / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / cytosol
Similarity search - Function
LisH / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / : / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily ...LisH / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / : / 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 / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Subunit (60 kDa) of TFIID and SAGA complexes / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 4 / Transcription initiation factor TFIID subunit 5
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsKolesnikova O / Ben-Shem A / Luo J / Ranish J / Schultz P / Papai G
Funding support United States, France, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P50 GM076547 RO1 GM110064 United States
French National Research AgencyANR-15-CE11-0022-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
CitationJournal: Nat Commun / Year: 2018
Title: Molecular structure of promoter-bound yeast TFIID.
Authors: Olga Kolesnikova / Adam Ben-Shem / Jie Luo / Jeff Ranish / Patrick Schultz / Gabor Papai /
Abstract: Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) ...Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.
History
DepositionSep 24, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseNov 21, 2018-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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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
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  • Surface view with fitted model
  • Atomic models: PDB-6hqa
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0251.png

Downloads & links

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Map

FileDownload / File: emd_0251.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKomagataella phaffii TFIID
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.014203308 - 0.022313362
Average (Standard dev.)0.000059873146 (±0.00071648543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0140.0220.000

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Supplemental data

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Mask #1

Fileemd_0251_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even half map

Fileemd_0251_half_map_1.map
Annotationeven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: odd half map

Fileemd_0251_half_map_2.map
Annotationodd half 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 : Transcription Factor IID

EntireName: Transcription Factor IID
Components
  • Complex: Transcription Factor IID
    • Protein or peptide: Taf2
    • 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: Taf8
    • Protein or peptide: Histone-fold
    • Protein or peptide: Histone-fold
    • Protein or peptide: Subunit (61/68 kDa) of TFIID and SAGA complexes
    • Protein or peptide: TFIID subunit (48 kDa)

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Supramolecule #1: Transcription Factor IID

SupramoleculeName: Transcription Factor IID / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Molecular weightTheoretical: 900 KDa

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Macromolecule #1: Taf2

MacromoleculeName: Taf2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Molecular weightTheoretical: 199.179078 KDa
SequenceString: MPAIPYDYPS IVSHGTPRKQ KSQAKSSRAT QNFKIAHQKV QLDVDLATQT VNGETELTIF ATDPSLSKVR LDARCMQIHE VSVNLIKAN FIAADFSRND EFQNDPNNET LQRIHRYQKS YDTNSESIDI YQHHFYRSKF NPLYLDLNDH ESPESVETLN T ENLTVYLP ...String:
MPAIPYDYPS IVSHGTPRKQ KSQAKSSRAT QNFKIAHQKV QLDVDLATQT VNGETELTIF ATDPSLSKVR LDARCMQIHE VSVNLIKAN FIAADFSRND EFQNDPNNET LQRIHRYQKS YDTNSESIDI YQHHFYRSKF NPLYLDLNDH ESPESVETLN T ENLTVYLP ENLRLRPHDL SNTYSPVSNY NSPLTSNSAL MNSDRLYTPF VLKINYSLRV PKNGIIFNGG SHTTIEKTQW FC HTINNDI GCSASSWMPC IDNFYEKYTW ELQLIVPKTV GDIGQTKPIG EKFSKQPNDN DDDDDDMIDS YQETDEEMTR EIK VVLPDF ESVKESPHIL DHSKKVVSVQ LYNNPVAAHH IGFFVGPFEQ LPASTFKFQD QSHPKILDGE ENNHSDFTAA VAAR VYFLP SQKEMVLNTC LALYKNLDFY SKEFGSYPFS TYSMVFVDNL PTQYSSFAGI SGISSEVLYD SGLVEPMFPV TELLS LIVA EQWSGINIVP KSLNDYWCVI GIAHFMAGQF LKKLFGFNNY KFVIKQRSDR ICREDIGKAP LANQHFRFPV NDATDF KFI RLKAPLVLFI LDRRMTKTDR SFGLSRVIPK IFAAAMSHDL YNGNCLSTSH FQHVCEKVAH HKLDSFFNNW VHNSGTP VL RVTQRFNKKR MFIEMGIRQV QGYELARSDA SKSRKKDPVS FLNEACQHVD QTGPGVTSQI FTGPMTIRIH EADGTPYE H IVDLKEGFTK LDIQYNTKYK RIKKNKKDEE LTKKDDSENT VNRLGDILSR SKDMQEWHLE DLSAEGEEAR TQDAAEWIR IDADFEWICQ IHLNQPDYMY QSQLQQDRDV EAQLDSVNFF SNSLRPNVFY SSVLVRTLMD NRYFYGVRCE AAKGLARLSK EENNHIGLH HLLKTLKQAF CYPMHDSHED ATTLINNPKN FLPLPNDFSD FQRLFIQETI PAALSTIKIK DSDLFLNLRR I LLRLLQYN DNLNNDFNDC FYVCSLIRAL ANTIVEAGMV LQDHNEGISY YDEATSEDGT LDDRINNINR ETVIEFNRRL QL DAADVSY HTCISDTILN EKVRLGSEGL INFRFPELLQ FTQEKYSVYV RLAGFRGLLL LGGLKNKSIL HYFFSTAKLE LSA LFKRGL IDHFLEAVGV AALFGTPSTL DDP(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)NKSRRDTYI RTTMKGAIQI LKRDYAIGEG LTKELWSAVH SCLLSINLKR DIFDLIDLMY DAYDSY LVK IDSVSDKKVV TRVETVGDNT AIVKLYAKPR PKPSIVDSTS QKIEEKPKIK LGFKKSTEKS SGLSLKIKPK NVEVPEK VR PSKVKKEIEP PKENGPSEKK IPPPSSLVDD VTAPTPKVED ISNHRSKKQL LVKFGYKTAN SRRFVRILLR EKRLEFSS I PFNPKRYDVK LKYNRELLEE RTRARVDEDQ NSSSNSYSMS IDGKATNSGP VDSLNDDSIP TDGVAELKPE VEQRKKRVA KSTPKARQSR TIESDQDALI SRSHKRQKFN PTINKPKSEE EIGENQTPEA GTQPTPKTKP KAKTKIKLKL KFLESMEMDE KTTGWRGGH VVEGLAGELE QLRARLEHHP QGQREPGGSE LKTAALAQHD EAVDNKFNKE QQNAFYEILH LPNLNEEQRN A FIQSLKDD PSQSANLLAE AKKLNDAQAP KVDNKFNKEQ QNAFYEILHL PNLNEEQRNA FIQSLKDDPS QSANLLAEAK KL NGAQAPK VDANSAGKST

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Macromolecule #2: Subunit (90 kDa) of TFIID and SAGA complexes

MacromoleculeName: Subunit (90 kDa) of TFIID and SAGA complexes / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
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

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Macromolecule #3: Subunit (60 kDa) of TFIID and SAGA complexes

MacromoleculeName: Subunit (60 kDa) of TFIID and SAGA complexes / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
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

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
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

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Macromolecule #5: Taf8

MacromoleculeName: Taf8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Molecular weightTheoretical: 6.400881 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)

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Macromolecule #6: Histone-fold

MacromoleculeName: Histone-fold / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Molecular weightTheoretical: 5.464728 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)

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Macromolecule #7: Histone-fold

MacromoleculeName: Histone-fold / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Molecular weightTheoretical: 5.805147 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)

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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)
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

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Macromolecule #9: TFIID subunit (48 kDa)

MacromoleculeName: TFIID subunit (48 kDa) / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Molecular weightTheoretical: 61.942883 KDa
SequenceString: MSRKPERRRQ PRLFSNDMRT LLFAYGDVQQ PQLETIQALE DVMIVFMTDL CHEAMTYATY QGRKHKLKME DFKFALRKDR LKLGRVEEL MNKQKEIQEA RKLFDSNEKE TKDDDIEKKR RKEAKRAIKE AKKLKLSKGD TAFMSSTPDG STPVDSGKRT S DQIDVGEY ...String:
MSRKPERRRQ PRLFSNDMRT LLFAYGDVQQ PQLETIQALE DVMIVFMTDL CHEAMTYATY QGRKHKLKME DFKFALRKDR LKLGRVEEL MNKQKEIQEA RKLFDSNEKE TKDDDIEKKR RKEAKRAIKE AKKLKLSKGD TAFMSSTPDG STPVDSGKRT S DQIDVGEY KRVKVERGNR SETVDSGLID MSNSVGASLD IPTPDQLNPT NTGVQTPSLH QPGESISAHS LSLPGETSVG GS TGISREN TPQVRPDVSV SQSSSQLHQR NESFPGLSVS KSTTSLNKDT MFDNRKRLLG NNGANPNGQK SSDPEKLSDA LTA AGVDLK EEESLLSQST VIQQSRRQLS TLSSFLHPVH LATFMRRVME NNGLRNYVDH DTELLSYMSS ACEGFMAGIL TDSV ILANH RKRPIKSKLK HSTTPRSDVS KVLRDIATKQ KEREEQRVQK RVTLDIEGQE DDGKSKQDNE EVLHRAANAT AMMMT SKSK KKKYSWMNAD SGAQGGKTNS VLARGDSGIR YRDAREEPGL VLRDLLGALE GRRMCVANTV VKGYARMND

UniProtKB: Transcription initiation factor TFIID subunit 4

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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

Concentration0.4 mg/mL
BufferpH: 8
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Equipped with Cs corrector / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 3-40 / 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: 4.9 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 45454 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 1.2 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

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Image processing

Particle selectionNumber selected: 295734
Startup modelType of model: OTHER / Details: Previous KpTFIID structure
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 180823
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 5 / Software - Name: RELION
FSC plot (resolution estimation)

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