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- EMDB-31115: TFIID lobe A subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-31115
TitleTFIID lobe A subcomplex
Map dataTFIID lobe A subcomplex
Sample
  • Complex: TFIID lobe A subcomplex
    • Protein or peptide: TATA-box-binding protein
    • Protein or peptide: Transcription initiation factor TFIID subunit 3
    • Protein or peptide: Transcription initiation factor TFIID subunit 4
    • Protein or peptide: Transcription initiation factor TFIID subunit 5
    • Protein or peptide: Transcription initiation factor TFIID subunit 6
    • Protein or peptide: Transcription initiation factor TFIID subunit 9
    • Protein or peptide: Transcription initiation factor TFIID subunit 10
    • Protein or peptide: Transcription initiation factor TFIID subunit 11
    • Protein or peptide: Transcription initiation factor TFIID subunit 12
    • Protein or peptide: Transcription initiation factor TFIID subunit 13
Function / homology
Function and homology information


SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / RNA polymerase transcription factor SL1 complex / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / positive regulation of response to cytokine stimulus / hepatocyte differentiation ...SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / RNA polymerase transcription factor SL1 complex / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / box C/D snoRNP assembly / male pronucleus / transcription regulator inhibitor activity / female pronucleus / positive regulation by host of viral transcription / SAGA complex / nuclear vitamin D receptor binding / RNA polymerase binding / RNA polymerase II general transcription initiation factor binding / limb development / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / response to L-glutamate / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / regulation of RNA splicing / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / MLL1 complex / RNA Polymerase I Transcription Initiation / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / TFIIB-class transcription factor binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / transcription by RNA polymerase III / somitogenesis / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / ovarian follicle development / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / nuclear estrogen receptor binding / promoter-specific chromatin binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / G1/S transition of mitotic cell cycle / multicellular organism growth / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / negative regulation of DNA-binding transcription factor activity / actin cytoskeleton / p53 binding / HATs acetylate histones / ATPase binding / spermatogenesis / nuclear membrane / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / transcription cis-regulatory region binding / Ub-specific processing proteases / chromatin remodeling / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / negative regulation of cell population proliferation / apoptotic process / DNA damage response / chromatin / nucleolus
Similarity search - Function
TAFII28-like protein domain / Transcription initiation factor TFIID subunit 11-like / hTAFII28-like protein conserved region / 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, subunit 13 / Transcription initiation factor IID, 18kD subunit / TAFH/NHR1 domain superfamily / NHR1 homology to TAF ...TAFII28-like protein domain / Transcription initiation factor TFIID subunit 11-like / hTAFII28-like protein conserved region / 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, subunit 13 / Transcription initiation factor IID, 18kD subunit / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TAF6, C-terminal HEAT repeat domain superfamily / 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 / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / 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. / TBP domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone-fold / Armadillo-type fold / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 4 / TATA-box-binding protein / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsChen X / Wu Z / Li J / Zhao D / Xu Y
CitationJournal: Science / Year: 2021
Title: Structural insights into preinitiation complex assembly on core promoters.
Authors: Xizi Chen / Yilun Qi / Zihan Wu / Xinxin Wang / Jiabei Li / Dan Zhao / Haifeng Hou / Yan Li / Zishuo Yu / Weida Liu / Mo Wang / Yulei Ren / Ze Li / Huirong Yang / Yanhui Xu /
Abstract: Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the ...Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.
History
DepositionMar 24, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.106
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.106
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7egf
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31115.png

Downloads & links

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Map

FileDownload / File: emd_31115.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTFIID lobe A subcomplex
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.106 / Movie #1: 0.106
Minimum - Maximum-2.7862208 - 4.942283
Average (Standard dev.)0.0023242235 (±0.064914405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z337.600337.600337.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-2.7864.9420.002

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Supplemental data

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Sample components

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Entire : TFIID lobe A subcomplex

EntireName: TFIID lobe A subcomplex
Components
  • Complex: TFIID lobe A subcomplex
    • Protein or peptide: TATA-box-binding protein
    • Protein or peptide: Transcription initiation factor TFIID subunit 3
    • Protein or peptide: Transcription initiation factor TFIID subunit 4
    • Protein or peptide: Transcription initiation factor TFIID subunit 5
    • Protein or peptide: Transcription initiation factor TFIID subunit 6
    • Protein or peptide: Transcription initiation factor TFIID subunit 9
    • Protein or peptide: Transcription initiation factor TFIID subunit 10
    • Protein or peptide: Transcription initiation factor TFIID subunit 11
    • Protein or peptide: Transcription initiation factor TFIID subunit 12
    • Protein or peptide: Transcription initiation factor TFIID subunit 13

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Supramolecule #1: TFIID lobe A subcomplex

SupramoleculeName: TFIID lobe A subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.729938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDQNNSLPPY AQGLASPQGA MTPGIPIFSP MMPYGTGLTP QPIQNTNSLS ILEEQQRQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQ QQQQQQAVAA AAVQQSTSQQ ATQGTSGQAP QLFHSQTLTT APLPGTTPLY PSPMTPMTPI TPATPASESS G IVPQLQNI ...String:
MDQNNSLPPY AQGLASPQGA MTPGIPIFSP MMPYGTGLTP QPIQNTNSLS ILEEQQRQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQ QQQQQQAVAA AAVQQSTSQQ ATQGTSGQAP QLFHSQTLTT APLPGTTPLY PSPMTPMTPI TPATPASESS G IVPQLQNI VSTVNLGCKL DLKTIALRAR NAEYNPKRFA AVIMRIREPR TTALIFSSGK MVCTGAKSEE QSRLAARKYA RV VQKLGFP AKFLDFKIQN MVGSCDVKFP IRLEGLVLTH QQFSSYEPEL FPGLIYRMIK PRIVLLIFVS GKVVLTGAKV RAE IYEAFE NIYPILKGFR KTT

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Macromolecule #2: Transcription initiation factor TFIID subunit 3

MacromoleculeName: Transcription initiation factor TFIID subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.76932 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCESYSRSLL RVSVAQICQA LGWDSVQLSA CHLLTDVLQR YLQQLGRGCH RYSELYGRTD PILDDVGEAF QLMGVSLHEL EDYIHNIEP VTFPHQIPSF PVSKNNVLQF PQPGSKDAEE RKEYIPDYLP PIVSSQEEEE EEQVPTDGGT SAEAMQVPLE E DDELEEEE ...String:
MCESYSRSLL RVSVAQICQA LGWDSVQLSA CHLLTDVLQR YLQQLGRGCH RYSELYGRTD PILDDVGEAF QLMGVSLHEL EDYIHNIEP VTFPHQIPSF PVSKNNVLQF PQPGSKDAEE RKEYIPDYLP PIVSSQEEEE EEQVPTDGGT SAEAMQVPLE E DDELEEEE IINDENFLGK RPLDSPEAEE LPAMKRPRLL STKGDTLDVV LLEAREPLSS INTQKIPPML SPVHVQDSTD LA PPSPEPP MLAPVAKSQM PTAKPLETKS FTPKTKTKTS SPGQKTKSPK TAQSPAMVGS PIRSPKTVSK EKKSPGRSKS PKS PKSPKV TTHIPQTPVR PETPNRTPSA TLSEKISKET IQVKQIQTPP DAGKLNSENQ PKKAVVADKT IEASIDAVIA RACA EREPD PFEFSSGSES EGDIFTSPKR ISGPECTTPK ASTSANNFTK SGSTPLPLSG GTSSSDNSWT MDASIDEVVR KAKLG TPSN MPPNFPYISS PSVSPPTPEP LHKVYEEKTK LPSSVEVKKK LKKELKTKMK KKEKQRDRER EKDKNKDKSK EKDKVK EKE KDKETGRETK YPWKEFLKEE EADPYKFKIK EFEDVDPKVK LKDGLVRKEK EKHKDKKKDR EKGKKDKDKR EKEKVKD KG REDKMKAPAP PLVLPPKELA LPLFSPATAS RVPAMLPSLL PVLPEKLFEE KEKVKEKEKK KDKKEKKKKK EKEKEKKE K EREKEKRERE KREKEKEKHK HEKIKVEPVA LAPSPVIPRL TLRVGAGQDK IVISKVVPAP EAKPAPSQNR PKTPPPAPA PAPGPMLVSP APVPLPLLAQ AAAGPALLPS PGPAASGASA KAPVRSVVTE TVSTYVIRDE WGNQIWICPG CNKPDDGSPM IGCDDCDDW YHWPCVGIMT APPEEMQWFC PKCANKKKDK KHKKRKHRAH

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Macromolecule #3: Transcription initiation factor TFIID subunit 4

MacromoleculeName: Transcription initiation factor TFIID subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110.221883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGSDLLDE VFFNSEVDEK VVSDLVGSLE SQLAASAAHH HHLAPRTPEV RAAAAGALGN HVVSGSPAGA AGAGPAAPAE GAPGAAPEP PPAGRARPGG GGPQRPGPPS PRRPLVPAGP APPAAKLRPP PEGSAGSCAP VPAAAAVAAG PEPAPAGPAK P AGPAALAA ...String:
MAAGSDLLDE VFFNSEVDEK VVSDLVGSLE SQLAASAAHH HHLAPRTPEV RAAAAGALGN HVVSGSPAGA AGAGPAAPAE GAPGAAPEP PPAGRARPGG GGPQRPGPPS PRRPLVPAGP APPAAKLRPP PEGSAGSCAP VPAAAAVAAG PEPAPAGPAK P AGPAALAA RAGPGPGPGP GPGPGPGPGK PAGPGAAQTL NGSAALLNSH HAAAPAVSLV NNGPAALLPL PKPAAPGTVI QT PPFVGAA APPAPAAPSP PAAPAPAAPA AAPPPPPPAP ATLARPPGHP AGPPTAAPAV PPPAAAQNGG SAGAAPAPAP AAG GPAGVS GQPGPGAAAA APAPGVKAES PKRVVQAAPP AAQTLAASGP ASTAASMVIG PTMQGALPSP AAVPPPAPGT PTGL PKGAA GAVTQSLSRT PTATTSGIRA TLTPTVLAPR LPQPPQNPTN IQNFQLPPGM VLVRSENGQL LMIPQQALAQ MQAQA HAQP QTTMAPRPAT PTSAPPVQIS TVQAPGTPII ARQVTPTTII KQVSQAQTTV QPSATLQRSP GVQPQLVLGG AAQTAS LGT ATAVQTGTPQ RTVPGATTTS SAATETMENV KKCKNFLSTL IKLASSGKQS TETAANVKEL VQNLLDGKIE AEDFTSR LY RELNSSPQPY LVPFLKRSLP ALRQLTPDSA AFIQQSQQQP PPPTSQATTA LTAVVLSSSV QRTAGKTAAT VTSALQPP V LSLTQPTQVG VGKQGQPTPL VIQQPPKPGA LIRPPQVTLT QTPMVALRQP HNRIMLTTPQ QIQLNPLQPV PVVKPAVLP GTKALSAVSA QAAAAQKNKL KEPGGGSFRD DDDINDVASM AGVNLSEESA RILATNSELV GTLTRSCKDE TFLLQAPLQR RILEIGKKH GITELHPDVV SYVSHATQQR LQNLVEKISE TAQQKNFSYK DDDRYEQASD VRAQLKFFEQ LDQIEKQRKD E QEREILMR AAKSRSRQED PEQLRLKQKA KEMQQQELAQ MRQRDANLTA LAAIGPRKKR KVDCPGPGSG AEGSGPGSVV PG SSGVGTP RQFTRQRITR VNLRDLIFCL ENERETSHSL LLYKAFLK

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Macromolecule #4: Transcription initiation factor TFIID subunit 5

MacromoleculeName: Transcription initiation factor TFIID subunit 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.932109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAALAEEQTE VAVKLEPEGP PTLLPPQAGD GAGEGSGGTT NNGPNGGGGN VAASSSTGGD GGTPKPTVAV SAAAPAGAAP VPAAAPDAG APHDRQTLLA VLQFLRQSKL REAEEALRRE AGLLEEAVAG SGAPGEVDSA GAEVTSALLS RVTASAPGPA A PDPPGTGA ...String:
MAALAEEQTE VAVKLEPEGP PTLLPPQAGD GAGEGSGGTT NNGPNGGGGN VAASSSTGGD GGTPKPTVAV SAAAPAGAAP VPAAAPDAG APHDRQTLLA VLQFLRQSKL REAEEALRRE AGLLEEAVAG SGAPGEVDSA GAEVTSALLS RVTASAPGPA A PDPPGTGA SGATVVSGSA SGPAAPGKVG SVAVEDQPDV SAVLSAYNQQ GDPTMYEEYY SGLKHFIECS LDCHRAELSQ LF YPLFVHM YLELVYNQHE NEAKSFFEKF HGDQECYYQD DLRVLSSLTK KEHMKGNETM LDFRTSKFVL RISRDSYQLL KRH LQEKQN NQIWNIVQEH LYIDIFDGMP RSKQQIDAMV GSLAGEAKRE ANKSKVFFGL LKEPEIEVPL DDEDEEGENE EGKP KKKKP KKDSIGSKSK KQDPNAPPQN RIPLPELKDS DKLDKIMNMK ETTKRVRLGP DCLPSICFYT FLNAYQGLTA VDVTD DSSL IAGGFADSTV RVWSVTPKKL RSVKQASDLS LIDKESDDVL ERIMDEKTAS ELKILYGHSG PVYGASFSPD RNYLLS SSE DGTVRLWSLQ TFTCLVGYKG HNYPVWDTQF SPYGYYFVSG GHDRVARLWA TDHYQPLRIF AGHLADVNCT RFHPNSN YV ATGSADRTVR LWDVLNGNCV RIFTGHKGPI HSLTFSPNGR FLATGATDGR VLLWDIGHGL MVGELKGHTD TVCSLRFS R DGEILASGSM DNTVRLWDAI KAFEDLETDD FTTATGHINL PENSQELLLG TYMTKSTPVV HLHFTRRNLV LAAGAYSPQ

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Macromolecule #5: Transcription initiation factor TFIID subunit 6

MacromoleculeName: Transcription initiation factor TFIID subunit 6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.749297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEEKKLKLS NTVLPSESMK VVAESMGIAQ IQEETCQLLT DEVSYRIKEI AQDALKFMHM GKRQKLTTSD IDYALKLKNV EPLYGFHAQ EFIPFRFASG GGRELYFYEE KEVDLSDIIN TPLPRVPLDV CLKAHWLSIE GCQPAIPENP PPAPKEQQKA E ATEPLKSA ...String:
MAEEKKLKLS NTVLPSESMK VVAESMGIAQ IQEETCQLLT DEVSYRIKEI AQDALKFMHM GKRQKLTTSD IDYALKLKNV EPLYGFHAQ EFIPFRFASG GGRELYFYEE KEVDLSDIIN TPLPRVPLDV CLKAHWLSIE GCQPAIPENP PPAPKEQQKA E ATEPLKSA KPGQEEDGPL KGKGQGATTA DGKGKEKKAP PLLEGAPLRL KPRSIHELSV EQQLYYKEIT EACVGSCEAK RA EALQSIA TDPGLYQMLP RFSTFISEGV RVNVVQNNLA LLIYLMRMVK ALMDNPTLYL EKYVHELIPA VMTCIVSRQL CLR PDVDNH WALRDFAARL VAQICKHFST TTNNIQSRIT KTFTKSWVDE KTPWTTRYGS IAGLAELGHD VIKTLILPRL QQEG ERIRS VLDGPVLSNI DRIGADHVQS LLLKHCAPVL AKLRPPPDNQ DAYRAEFGSL GPLLCSQVVK ARAQAALQAQ QVNRT TLTI TQPRPTLTLS QAPQPGPRTP GLLKVPGSIA LPVQTLVSAR AAAPPQPSPP PTKFIVMSSS SSAPSTQQVL SLSTSA PGS GSTTTSPVTT TVPSVQPIVK LVSTATTAPP STAPSGPGSV QKYIVVSLPP TGEGKGGPTS HPSPVPPPAS SPSPLSG SA LCGGKQEAGD SPPPAPGTPK ANGSQPNSGS PQPAP

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Macromolecule #6: Transcription initiation factor TFIID subunit 9

MacromoleculeName: Transcription initiation factor TFIID subunit 9 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.006838 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MESGKTASPK SMPKDAQMMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKATVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQR NQTPLPLIKP YSGPRLPPDR YCLTAPNYRL KSLQKKASTS AGRITVPRLS VGSVTSRPST P TLGTPTPQ ...String:
MESGKTASPK SMPKDAQMMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKATVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQR NQTPLPLIKP YSGPRLPPDR YCLTAPNYRL KSLQKKASTS AGRITVPRLS VGSVTSRPST P TLGTPTPQ TMSVSTKVGT PMSLTGQRFT VQMPTSQSPA VKASIPATSA VQNVLINPSL IGSKNILITT NMMSSQNTAN ES SNALKRK REDDDDDDDD DDDYDNL

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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: Homo sapiens (human)
Molecular weightTheoretical: 21.731248 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN ...String:
MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN DALQHCKMKG TASGSSRSKS KDRKYTLTME DLTPALSEYG INVKKPHYFT

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Macromolecule #8: Transcription initiation factor TFIID subunit 11

MacromoleculeName: Transcription initiation factor TFIID subunit 11 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.340094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDAHESPSD KGGETGESDE TAAVPGDPGA TDTDGIPEET DGDADVDLKE AAAEEGELES QDVSDLTTVE REDSSLLNPA AKKLKIDTK EKKEKKQKVD EDEIQKMQIL VSSFSEEQLN RYEMYRRSAF PKAAIKRLIQ SITGTSVSQN VVIAMSGISK V FVGEVVEE ...String:
MDDAHESPSD KGGETGESDE TAAVPGDPGA TDTDGIPEET DGDADVDLKE AAAEEGELES QDVSDLTTVE REDSSLLNPA AKKLKIDTK EKKEKKQKVD EDEIQKMQIL VSSFSEEQLN RYEMYRRSAF PKAAIKRLIQ SITGTSVSQN VVIAMSGISK V FVGEVVEE ALDVCEKWGE MPPLQPKHMR EAVRRLKSKG QIPNSKHKKI IFF

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Macromolecule #9: Transcription initiation factor TFIID subunit 12

MacromoleculeName: Transcription initiation factor TFIID subunit 12 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.948467 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MNQFGPSALI NLSNFSSIKP EPASTPPQGS MANSTAVVKI PGTPGAGGRL SPENNQVLTK KKLQDLVREV DPNEQLDEDV EEMLLQIAD DFIESVVTAA CQLARHRKSS TLEVKDVQLH LERQWNMWIP GFGSEEIRPY KKACTTEAHK QRMALIRKTT K K

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Macromolecule #10: Transcription initiation factor TFIID subunit 13

MacromoleculeName: Transcription initiation factor TFIID subunit 13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.307068 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADEEEDPTF EEENEEIGGG AEGGQGKRKR LFSKELRCMM YGFGDDQNPY TESVDILEDL VIEFITEMTH KAMSIGRQGR VQVEDIVFL IRKDPRKFAR VKDLLTMNEE LKRARKAFDE ANYGS

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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

BufferpH: 7.9
GridMaterial: GOLD
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15078

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7egf:
TFIID lobe A subcomplex

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