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- EMDB-31117: TFIID lobe C subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-31117
TitleTFIID lobe C subcomplex
Map dataTFIID lobe C subcomplex
Sample
  • Complex: TFIID lobe C subcomplex
    • Protein or peptide: Transcription initiation factor TFIID subunit 1
    • Protein or peptide: Transcription initiation factor TFIID subunit 2
    • Protein or peptide: Transcription initiation factor TFIID subunit 6
    • Protein or peptide: Transcription initiation factor TFIID subunit 7
    • Protein or peptide: Transcription initiation factor TFIID subunit 8
    • DNA: DNA (45-MER)
    • DNA: DNA (45-MER)
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / DNA-templated transcription open complex formation / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex ...spermine transport / negative regulation of MHC class I biosynthetic process / DNA-templated transcription open complex formation / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / maintenance of protein location in nucleus / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / SAGA complex / nuclear vitamin D receptor binding / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / cellular response to ATP / regulation of fat cell differentiation / inner cell mass cell proliferation / histone acetyltransferase binding / midbrain development / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 / ubiquitin conjugating enzyme activity / MLL1 complex / transcription initiation at RNA polymerase I promoter / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / P-TEFb complex binding / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / intracellular estrogen receptor signaling pathway / regulation of DNA repair / positive regulation of intrinsic apoptotic signaling pathway / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / regulation of signal transduction by p53 class mediator / male germ cell nucleus / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / response to organic cyclic compound / protein polyubiquitination / cellular response to UV / G2/M transition of mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / protein autophosphorylation / cell differentiation / transcription coactivator activity / protein stabilization / transcription cis-regulatory region binding / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex
Similarity search - Function
TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins ...TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 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 12, 2021-
Map releaseMay 12, 2021-
UpdateMay 12, 2021-
Current statusMay 12, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.222
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.222
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7egh
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31117.png

Downloads & links

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Map

FileDownload / File: emd_31117.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTFIID lobe C subcomplex
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.222 / Movie #1: 0.222
Minimum - Maximum-3.1059234 - 5.395505
Average (Standard dev.)0.0013952557 (±0.045913033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 540.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z540.160540.160540.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-3.1065.3960.001

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Supplemental data

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Sample components

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Entire : TFIID lobe C subcomplex

EntireName: TFIID lobe C subcomplex
Components
  • Complex: TFIID lobe C subcomplex
    • Protein or peptide: Transcription initiation factor TFIID subunit 1
    • Protein or peptide: Transcription initiation factor TFIID subunit 2
    • Protein or peptide: Transcription initiation factor TFIID subunit 6
    • Protein or peptide: Transcription initiation factor TFIID subunit 7
    • Protein or peptide: Transcription initiation factor TFIID subunit 8
    • DNA: DNA (45-MER)
    • DNA: DNA (45-MER)

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Supramolecule #1: TFIID lobe C subcomplex

SupramoleculeName: TFIID lobe C 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: Transcription initiation factor TFIID subunit 1

MacromoleculeName: Transcription initiation factor TFIID subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 212.956172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGPGCDLLLR TAATITAAAI MSDTDSDEDS AGGGPFSLAG FLFGNINGAG QLEGESVLDD ECKKHLAGLG ALGLGSLITE LTANEELTG TDGALVNDEG WVRSTEDAVD YSDINEVAED ESRRYQQTMG SLQPLCHSDY DEDDYDADCE DIDCKLMPPP P PPPGPMKK ...String:
MGPGCDLLLR TAATITAAAI MSDTDSDEDS AGGGPFSLAG FLFGNINGAG QLEGESVLDD ECKKHLAGLG ALGLGSLITE LTANEELTG TDGALVNDEG WVRSTEDAVD YSDINEVAED ESRRYQQTMG SLQPLCHSDY DEDDYDADCE DIDCKLMPPP P PPPGPMKK DKDQDSITGE KVDFSSSSDS ESEMGPQEAT QAESEDGKLT LPLAGIMQHD ATKLLPSVTE LFPEFRPGKV LR FLRLFGP GKNVPSVWRS ARRKRKKKHR ELIQEEQIQE VECSVESEVS QKSLWNYDYA PPPPPEQCLS DDEITMMAPV ESK FSQSTG DIDKVTDTKP RVAEWRYGPA RLWYDMLGVP EDGSGFDYGF KLRKTEHEPV IKSRMIEEFR KLEENNGTDL LADE NFLMV TQLHWEDDII WDGEDVKHKG TKPQRASLAG WLPSSMTRNA MAYNVQQGFA ATLDDDKPWY SIFPIDNEDL VYGRW EDNI IWDAQAMPRL LEPPVLTLDP NDENLILEIP DEKEEATSNS PSKESKKESS LKKSRILLGK TGVIKEEPQQ NMSQPE VKD PWNLSNDEYY YPKQQGLRGT FGGNIIQHSI PAVELRQPFF PTHMGPIKLR QFHRPPLKKY SFGALSQPGP HSVQPLL KH IKKKAKMREQ ERQASGGGEM FFMRTPQDLT GKDGDLILAE YSEENGPLMM QVGMATKIKN YYKRKPGKDP GAPDCKYG E TVYCHTSPFL GSLHPGQLLQ AFENNLFRAP IYLHKMPETD FLIIRTRQGY YIRELVDIFV VGQQCPLFEV PGPNSKRAN THIRDFLQVF IYRLFWKSKD RPRRIRMEDI KKAFPSHSES SIRKRLKLCA DFKRTGMDSN WWVLKSDFRL PTEEEIRAMV SPEQCCAYY SMIAAEQRLK DAGYGEKSFF APEEENEEDF QMKIDDEVRT APWNTTRAFI AAMKGKCLLE VTGVADPTGC G EGFSYVKI PNKPTQQKDD KEPQPVKKTV TGTDADLRRL SLKNAKQLLR KFGVPEEEIK KLSRWEVIDV VRTMSTEQAR SG EGPMSKF ARGSRFSVAE HQERYKEECQ RIFDLQNKVL SSTEVLSTDT DSSSAEDSDF EEMGKNIENM LQNKKTSSQL SRE REEQER KELQRMLLAA GSAASGNNHR DDDTASVTSL NSSATGRCLK IYRTFRDEEG KEYVRCETVR KPAVIDAYVR IRTT KDEEF IRKFALFDEQ HREEMRKERR RIQEQLRRLK RNQEKEKLKG PPEKKPKKMK ERPDLKLKCG ACGAIGHMRT NKFCP LYYQ TNAPPSNPVA MTEEQEEELE KTVIHNDNEE LIKVEGTKIV LGKQLIESAD EVRRKSLVLK FPKQQLPPKK KRRVGT TVH CDYLNRPHKS IHRRRTDPMV TLSSILESII NDMRDLPNTY PFHTPVNAKV VKDYYKIITR PMDLQTLREN VRKRLYP SR EEFREHLELI VKNSATYNGP KHSLTQISQS MLDLCDEKLK EKEDKLARLE KAINPLLDDD DQVAFSFILD NIVTQKMM A VPDSWPFHHP VNKKFVPDYY KVIVNPMDLE TIRKNISKHK YQSRESFLDD VNLILANSVK YNGPESQYTK TAQEIVNVC YQTLTEYDEH LTQLEKDICT AKEAALEEAE LESLDPMTPG PYTPQPPDLY DTNTSLSMSR DASVFQDESN MSVLDIPSAT PEKQVTQEG EDGDGDLADE EEGTVQQPQA SVLYEDLLMS EGEDDEEDAG SDEEGDNPFS AIQLSESGSD SDVGSGGIRP K QPRMLQEN TRMDMENEES MMSYEGDGGE ASHGLEDSNI SYGSYEEPDP KSNTQDTSFS SIGGYEVSEE EEDEEEEEQR SG PSVLSQV HLSEDEEDSE DFHSIAGDSD LDSDE

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Macromolecule #2: Transcription initiation factor TFIID subunit 2

MacromoleculeName: Transcription initiation factor TFIID subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.159984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPLTGVEPAR MNRKKGDKGF ESPRPYKLTH QVVCINNINF QRKSVVGFVE LTIFPTVANL NRIKLNSKQC RIYRVRINDL EAAFIYNDP TLEVCHSESK QRNLNYFSNA YAAAVSAVDP DAGNGELCIK VPSELWKHVD ELKVLKIHIN FSLDQPKGGL H FVVPSVEG ...String:
MPLTGVEPAR MNRKKGDKGF ESPRPYKLTH QVVCINNINF QRKSVVGFVE LTIFPTVANL NRIKLNSKQC RIYRVRINDL EAAFIYNDP TLEVCHSESK QRNLNYFSNA YAAAVSAVDP DAGNGELCIK VPSELWKHVD ELKVLKIHIN FSLDQPKGGL H FVVPSVEG SMAERGAHVF SCGYQNSTRF WFPCVDSYSE LCTWKLEFTV DAAMVAVSNG DLVETVYTHD MRKKTFHYML TI PTAASNI SLAIGPFEIL VDPYMHEVTH FCLPQLLPLL KHTTSYLHEV FEFYEEILTC RYPYSCFKTV FIDEAYVEVA AYA SMSIFS TNLLHSAMII DETPLTRRCL AQSLAQQFFG CFISRMSWSD EWVLKGISGY IYGLWMKKTF GVNEYRHWIK EELD KIVAY ELKTGGVLLH PIFGGGKEKD NPASHLHFSI KHPHTLSWEY YSMFQCKAHL VMRLIENRIS MEFMLQVFNK LLSLA STAS SQKFQSHMWS QMLVSTSGFL KSISNVSGKD IQPLIKQWVD QSGVVKFYGS FAFNRKRNVL ELEIKQDYTS PGTQKY VGP LKVTVQELDG SFNHTLQIEE NSLKHDIPCH SKSRRNKKKK IPLMNGEEVD MDLSAMDADS PLLWIRIDPD MSVLRKV EF EQADFMWQYQ LRYERDVVAQ QESILALEKF PTPASRLALT DILEQEQCFY RVRMSACFCL AKIANSMVST WTGPPAMK S LFTRMFCCKS CPNIVKTNNF MSFQSYFLQK TMPVAMALLR DVHNLCPKEV LTFILDLIKY NDNRKNKFSD NYYRAEMID ALANSVTPAV SVNNEVRTLD NLNPDVRLIL EEITRFLNME KLLPSYRHTI TVSCLRAIRV LQKNGHVPSD PALFKSYAEY GHFVDIRIA ALEAVVDYTK VDRSYEELQW LLNMIQNDPV PYVRHKILNM LTKNPPFTKN MESPLCNEAL VDQLWKLMNS G TSHDWRLR CGAVDLYFTL FGLSRPSCLP LPELGLVLNL KEKKAVLNPT IIPESVAGNQ EAANNPSSHP QLVGFQNPFS SS QDEEEID MDTVHDSQAF ISHHLNMLER PSTPGLSKYR PASSRSALIP QHSAGCDSTP TTKPQWSLEL ARKGTGKEQA PLE MSMHPA ASAPLSVFTK ESTASKHSDH HHHHHHEHKK KKKKHKHKHK HKHKHDSKEK DKEPFTFSSP ASGRSIRSPS LSD

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Macromolecule #3: Transcription initiation factor TFIID subunit 6

MacromoleculeName: Transcription initiation factor TFIID subunit 6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #4: Transcription initiation factor TFIID subunit 7

MacromoleculeName: Transcription initiation factor TFIID subunit 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.325117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKSKDDAPH ELESQFILRL PPEYASTVRR AVQSGHVNLK DRLTIELHPD GRHGIVRVDR VPLASKLVDL PCVMESLKTI DKKTFYKTA DICQMLVSTV DGDLYPPVEE PVASTDPKAS KKKDKDKEKK FIWNHGITLP LKNVRKRRFR KTAKKKYIES P DVEKEVKR ...String:
MSKSKDDAPH ELESQFILRL PPEYASTVRR AVQSGHVNLK DRLTIELHPD GRHGIVRVDR VPLASKLVDL PCVMESLKTI DKKTFYKTA DICQMLVSTV DGDLYPPVEE PVASTDPKAS KKKDKDKEKK FIWNHGITLP LKNVRKRRFR KTAKKKYIES P DVEKEVKR LLSTDAEAVS TRWEIIAEDE TKEAENQGLD ISSPGMSGHR QGHDSLEHDE LREIFNDLSS SSEDEDETQH QD EEDINII DTEEDLERQL QDKLNESDEQ HQENEGTNQL VMGIQKQIDN MKGKLQETQD RAKRQEDLIM KVENLALKNR FQA VLDELK QKEDREKEQL SSLQEELESL LEK

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Macromolecule #5: Transcription initiation factor TFIID subunit 8

MacromoleculeName: Transcription initiation factor TFIID subunit 8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.304359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADAAATAGA GGSGTRSGSK QSTNPADNYH LARRRTLQVV VSSLLTEAGF ESAEKASVET LTEMLQSYIS EIGRSAKSYC EHTARTQPT LSDIVVTLVE MGFNVDTLPA YAKRSQRMVI TAPPVTNQPV TPKALTAGQN RPHPPHIPSH FPEFPDPHTY I KTPTYREP ...String:
MADAAATAGA GGSGTRSGSK QSTNPADNYH LARRRTLQVV VSSLLTEAGF ESAEKASVET LTEMLQSYIS EIGRSAKSYC EHTARTQPT LSDIVVTLVE MGFNVDTLPA YAKRSQRMVI TAPPVTNQPV TPKALTAGQN RPHPPHIPSH FPEFPDPHTY I KTPTYREP VSDYQVLREK AASQRRDVER ALTRFMAKTG ETQSLFKDDV STFPLIAARP FTIPYLTALL PSELEMQQME ET DSSEQDE QTDTENLALH ISMEDSGAEK ENTSVLQQNP SLSGSRNGEE NIIDNPYLRP VKKPKIRRKK SLS

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Macromolecule #6: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.317238 KDa
SequenceString: (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT)(DC) (DC)(DT)(DC)(DA)(DG)(DT)(DC)(DG)(DC)(DG) (DA) (DT)(DC)(DG)(DA)(DA)(DC) ...String:
(DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT)(DC) (DC)(DT)(DC)(DA)(DG)(DT)(DC)(DG)(DC)(DG) (DA) (DT)(DC)(DG)(DA)(DA)(DC)(DA)(DC) (DT)(DC)(DG)(DA)(DG)(DC)(DC)(DG)(DA)(DG) (DC)(DA) (DG)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DA)(DC)(DG)

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Macromolecule #7: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.814336 KDa
SequenceString: (DA)(DT)(DC)(DC)(DA)(DT)(DG)(DG)(DT)(DC) (DC)(DG)(DT)(DA)(DG)(DG)(DC)(DA)(DC)(DG) (DT)(DC)(DT)(DG)(DC)(DT)(DC)(DG)(DG) (DC)(DT)(DC)(DG)(DA)(DG)(DT)(DG)(DT)(DT) (DC) (DG)(DA)(DT)(DC)(DG)(DC) ...String:
(DA)(DT)(DC)(DC)(DA)(DT)(DG)(DG)(DT)(DC) (DC)(DG)(DT)(DA)(DG)(DG)(DC)(DA)(DC)(DG) (DT)(DC)(DT)(DG)(DC)(DT)(DC)(DG)(DG) (DC)(DT)(DC)(DG)(DA)(DG)(DT)(DG)(DT)(DT) (DC) (DG)(DA)(DT)(DC)(DG)(DC)(DG)(DA) (DC)(DT)(DG)(DA)(DG)(DG)(DA)(DC)(DG)(DA) (DA)(DC) (DG)(DC)(DG)(DC)(DC)(DC)(DC) (DC)(DA)(DC)(DC)(DC)(DC)(DC)(DT)(DT)(DT) (DT)(DA)(DT) (DA)(DG)(DG)(DC)(DG)(DC) (DC)(DC)(DT)(DT)(DC)(DG)(DA)(DT)

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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 / Pretreatment - Type: PLASMA CLEANING
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 / Cs: 2.7 mm
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: 50.0 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: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121285

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7egh:
TFIID lobe C subcomplex

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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

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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

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