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- EMDB-18612: Structure of TRRAP and EP400 in the human Tip 60 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-18612
TitleStructure of TRRAP and EP400 in the human Tip 60 complex
Map dataTRRAPP and EP400 in the Tip60 complex
Sample
  • Cell: Human Tip60 complex
    • Protein or peptide: TRRAP
    • Protein or peptide: EP400
KeywordsEukaryotic transcription / Histone acetyltransferase / chromatin remodeling / Complex / TRANSCRIPTION
Function / homology
Function and homology information


transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / ATP-dependent chromatin remodeler activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / NuA4 histone acetyltransferase complex / regulation of RNA splicing / positive regulation of double-strand break repair via homologous recombination ...transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / ATP-dependent chromatin remodeler activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / NuA4 histone acetyltransferase complex / regulation of RNA splicing / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / helicase activity / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage/Telomere Stress Induced Senescence / nucleosome / chromatin organization / HATs acetylate histones / regulation of apoptotic process / regulation of cell cycle / Ub-specific processing proteases / hydrolase activity / nuclear speck / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain ...E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / PIK-related kinase, FAT / FATC / FAT domain / FAT domain profile. / FATC domain profile. / FATC domain / PIK-related kinase / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT/Myb domain / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Helicase conserved C-terminal domain / Armadillo-like helical / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E1A-binding protein p400 / Transformation/transcription domain-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsLi C / Smirnova E / Schnitzler C / Crucifix C / Concordet JP / Brion A / Poterszman A / Schultz P / Papai G / Ben-Shem A
Funding support France, 1 items
OrganizationGrant numberCountry
La ligue contre le cancer France
CitationJournal: Nature / Year: 2024
Title: Structure of the human TIP60-C histone exchange and acetyltransferase complex.
Authors: Changqing Li / Ekaterina Smirnova / Charlotte Schnitzler / Corinne Crucifix / Jean Paul Concordet / Alice Brion / Arnaud Poterszman / Patrick Schultz / Gabor Papai / Adam Ben-Shem /
Abstract: Chromatin structure is a key regulator of DNA transcription, replication and repair. In humans, the TIP60-EP400 complex (TIP60-C) is a 20-subunit assembly that affects chromatin structure through two ...Chromatin structure is a key regulator of DNA transcription, replication and repair. In humans, the TIP60-EP400 complex (TIP60-C) is a 20-subunit assembly that affects chromatin structure through two enzymatic activities: ATP-dependent exchange of histone H2A-H2B for H2A.Z-H2B, and histone acetylation. In yeast, however, these activities are performed by two independent complexes-SWR1 and NuA4, respectively. How the activities of the two complexes are merged into one supercomplex in humans, and what this association entails for the structure and mechanism of the proteins and their recruitment to chromatin, are unknown. Here we describe the structure of the endogenous human TIP60-C. We find a three-lobed architecture composed of SWR1-like (SWR1L) and NuA4-like (NuA4L) parts, which associate with a TRRAP activator-binding module. The huge EP400 subunit contains the ATPase motor, traverses the junction between SWR1L and NuA4L twice and constitutes the scaffold of the three-lobed architecture. NuA4L is completely rearranged compared with its yeast counterpart. TRRAP is flexibly tethered to NuA4L-in stark contrast to its robust connection to the completely opposite side of NuA4 in yeast. A modelled nucleosome bound to SWR1L, supported by tests of TIP60-C activity, suggests that some aspects of the histone exchange mechanism diverge from what is seen in yeast. Furthermore, a fixed actin module (as opposed to the mobile actin subcomplex in SWR1; ref. ), the flexibility of TRRAP and the weak effect of extranucleosomal DNA on exchange activity lead to a different, activator-based mode of enlisting TIP60-C to chromatin.
History
DepositionOct 6, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18612.png

Downloads & links

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Map

FileDownload / File: emd_18612.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRRAPP and EP400 in the Tip60 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 560 pix.
= 482.72 Å		0.86 Å/pix.
x 560 pix.
= 482.72 Å		0.86 Å/pix.
x 560 pix.
= 482.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.112
Minimum - Maximum-0.1283481 - 0.44453797
Average (Standard dev.)0.00053124933 (±0.010329361)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 482.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18612_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_18612_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_18612_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Human Tip60 complex

EntireName: Human Tip60 complex
Components
  • Cell: Human Tip60 complex
    • Protein or peptide: TRRAP
    • Protein or peptide: EP400

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Supramolecule #1: Human Tip60 complex

SupramoleculeName: Human Tip60 complex / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TRRAP

MacromoleculeName: TRRAP / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQLR KLVLEIIHRI PTNEHLRPHT KNVLSVMFRF LETENEENVL ICLRIIIELH KQFRPPITQE IHHFLDFVKQ IYKELPKVVN ...String:
MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQLR KLVLEIIHRI PTNEHLRPHT KNVLSVMFRF LETENEENVL ICLRIIIELH KQFRPPITQE IHHFLDFVKQ IYKELPKVVN RYFENPQVIP ENTVPPPEMV GMITTIAVKV NPEREDSETR THSIIPRGSL SLKVLAELPI IVVLMYQLYK LNIHNVVAEF VPLIMNTIAI QVSAQARQHK LYNKELYADF IAAQIKTLSF LAYIIRIYQE LVTKYSQQMV KGMLQLLSNC PAETAHLRKE LLIAAKHILT TELRNQFIPC MDKLFDESIL IGSGYTARET LRPLAYSTLA DLVHHVRQHL PLSDLSLAVQ LFAKNIDDES LPSSIQTMSC KLLLNLVDCI RSKSEQESGN GRDVLMRMLE VFVLKFHTIA RYQLSAIFKK CKPQSELGAV EAALPGVPTA PAAPGPAPSP APVPAPPPPP PPPPPATPVT PAPVPPFEKQ GEKDKEDKQT FQVTDCRSLV KTLVCGVKTI TWGITSCKAP GEAQFIPNKQ LQPKETQIYI KLVKYAMQAL DIYQVQIAGN GQTYIRVANC QTVRMKEEKE VLEHFAGVFT MMNPLTFKEI FQTTVPYMVE RISKNYALQI VANSFLANPT TSALFATILV EYLLDRLPEM GSNVELSNLY LKLFKLVFGS VSLFAAENEQ MLKPHLHKIV NSSMELAQTA KEPYNYFLLL RALFRSIGGG SHDLLYQEFL PLLPNLLQGL NMLQSGLHKQ HMKDLFVELC LTVPVRLSSL LPYLPMLMDP LVSALNGSQT LVSQGLRTLE LCVDNLQPDF LYDHIQPVRA ELMQALWRTL RNPADSISHV AYRVLGKFGG SNRKMLKESQ KLHYVVTEVQ GPSITVEFSD CKASLQLPME KAIETALDCL KSANTEPYYR RQAWEVIKCF LVAMMSLEDN KHALYQLLAH PNFTEKTIPN VIISHRYKAQ DTPARKTFEQ ALTGAFMSAV IKDLRPSALP FVASLIRHYT MVAVAQQCGP FLLPCYQVGS QPSTAMFHSE ENGSKGMDPL VLIDAIAICM AYEEKELCKI GEVALAVIFD VASIILGSKE RACQLPLFSY IVERLCACCY EQAWYAKLGG VVSIKFLMER LPLTWVLQNQ QTFLKALLFV MMDLTGEVSN GAVAMAKTTL EQLLMRCATP LKDEERAEEI VAAQEKSFHH VTHDLVREVT SPNSTVRKQA MHSLQVLAQV TGKSVTVIME PHKEVLQDMV PPKKHLLRHQ PANAQIGLME GNTFCTTLQP RLFTMDLNVV EHKVFYTELL NLCEAEDSAL TKLPCYKSLP SLVPLRIAAL NALAACNYLP QSREKIIAAL FKALNSTNSE LQEAGEACMR KFLEGATIEV DQIHTHMRPL LMMLGDYRSL TLNVVNRLTS VTRLFPNSFN DKFCDQMMQH LRKWMEVVVI THKGGQRSDG NESISECGRC PLSPFCQFEE MKICSAIINL FHLIPAAPQT LVKPLLEVVM KTERAMLIEA GSPFREPLIK FLTRHPSQTV ELFMMEATLN DPQWSRMFMS FLKHKDARPL RDVLAANPNR FITLLLPGGA QTAVRPGSPS TSTMRLDLQF QAIKIISIIV KNDDSWLASQ HSLVSQLRRV WVSENFQERH RKENMAATNW KEPKLLAYCL LNYCKRNYGD IELLFQLLRA FTGRFLCNMT FLKEYMEEEI PKNYSIAQKR ALFFRFVDFN DPNFGDELKA KVLQHILNPA FLYSFEKGEG EQLLGPPNPE GDNPESITSV FITKVLDPEK QADMLDSLRI YLLQYATLLV EHAPHHIHDN NKNRNSKLRR LMTFAWPCLL SKACVDPACK YSGHLLLAHI IAKFAIHKKI VLQVFHSLLK AHAMEARAIV RQAMAILTPA VPARMEDGHQ MLTHWTRKII VEEGHTVPQL VHILHLIVQH FKVYYPVRHH LVQHMVSAMQ RLGFTPSVTI EQRRLAVDLS EVVIKWELQR IKDQQPDSDM DPNSSGEGVN SVSSSIKRGL SVDSAQEVKR FRTATGAISA VFGRSQSLPG ADSLLAKPID KQHTDTVVNF LIRVACQVND NTNTAGSPGE VLSRRCVNLL KTALRPDMWP KSELKLQWFD KLLMTVEQPN QVNYGNICTG LEVLSFLLTV LQSPAILSSF KPLQRGIAAC MTCGNTKVLR AVHSLLSRLM SIFPTEPSTS SVASKYEELE CLYAAVGKVI YEGLTNYEKA TNANPSQLFG TLMILKSACS NNPSYIDRLI SVFMRSLQKM VREHLNPQAA SGSTEATSGT SELVMLSLEL VKTRLAVMSM EMRKNFIQAI LTSLIEKSPD AKILRAVVKI VEEWVKNNSP MAANQTPTLR EKSILLVKMM TYIEKRFPED LELNAQFLDL VNYVYRDETL SGSELTAKLE PAFLSGLRCA QPLIRAKFFE VFDNSMKRRV YERLLYVTCS QNWEAMGNHF WIKQCIELLL AVCEKSTPIG TSCQGAMLPS ITNVINLADS HDRAAFAMVT HVKQEPRERE NSESKEEDVE IDIELAPGDQ TSTPKTKELS EKDIGNQLHM LTNRHDKFLD TLREVKTGAL LSAFVQLCHI STTLAEKTWV QLFPRLWKIL SDRQQHALAG EISPFLCSGS HQVQRDCQPS ALNCFVEAMS QCVPPIPIRP CVLKYLGKTH NLWFRSTLML EHQAFEKGLS LQIKPKQTTE FYEQESITPP QQEILDSLAE LYSLLQEEDM WAGLWQKRCK YSETATAIAY EQHGFFEQAQ ESYEKAMDKA KKEHERSNAS PAIFPEYQLW EDHWIRCSKE LNQWEALTEY GQSKGHINPY LVLECAWRVS NWTAMKEALV QVEVSCPKEM AWKVNMYRGY LAICHPEEQQ LSFIERLVEM ASSLAIREWR RLPHVVSHVH TPLLQAAQQI IELQEAAQIN AGLQPTNLGR NNSLHDMKTV VKTWRNRLPI VSDDLSHWSS IFMWRQHHYQ GKPTWSGMHS SSIVTAYENS SQHDPSSNNA MLGVHASASA IIQYGKIARK QGLVNVALDI LSRIHTIPTV PIVDCFQKIR QQVKCYLQLA GVMGKNECMQ GLEVIESTNL KYFTKEMTAE FYALKGMFLA QINKSEEANK AFSAAVQMHD VLVKAWAMWG DYLENIFVKE RQLHLGVSAI TCYLHACRHQ NESKSRKYLA KVLWLLSFDD DKNTLADAVD KYCIGVPPIQ WLAWIPQLLT CLVGSEGKLL LNLISQVGRV YPQAVYFPIR TLYLTLKIEQ RERYKSDPGP IRATAPMWRC SRIMHMQREL HPTLLSSLEG IVDQMVWFRE NWHEEVLRQL QQGLAKCYSV AFEKSGAVSD AKITPHTLNF VKKLVSTFGV GLENVSNVST MFSSAASESL ARRAQATAQD PVFQKLKGQF TTDFDFSVPG SMKLHNLISK LKKWIKILEA KTKQLPKFFL IEEKCRFLSN FSAQTAEVEI PGEFLMPKPT HYYIKIARFM PRVEIVQKHN TAARRLYIRG HNGKIYPYLV MNDACLTESR REERVLQLLR LLNPCLEKRK ETTKRHLFFT VPRVVAVSPQ MRLVEDNPSS LSLVEIYKQR CAKKGIEHDN PISRYYDRLA TVQARGTQAS HQVLRDILKE VQSNMVPRSM LKEWALHTFP NATDYWTFRK MFTIQLALIG FAEFVLHLNR LNPEMLQIAQ DTGKLNVAYF RFDINDATGD LDANRPVPFR LTPNISEFLT TIGVSGPLTA SMIAVARCFA QPNFKVDGIL KTVLRDEIIA WHKKTQEDTS SPLSAAGQPE NMDSQQLVSL VQKAVTAIMT RLHNLAQFEG GESKVNTLVA AANSLDNLCR MDPAWHPWL

UniProtKB: Transformation/transcription domain-associated protein

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Macromolecule #2: EP400

MacromoleculeName: EP400 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHHGTGPQNV QHQLQRSRAC PGSEGEEQPA HPNPPPSPAA PFAPSASPSA PQSPSYQIQQ LMNRSPATGQ NVNITLQSVG PVVGGNQQIT LAPLPLPSPT SPGFQFSAQP RRFEHGSPSY IQVTSPLSQQ VQTQSPTQPS PGPGQALQNV RAGAPGPGLG LCSSSPTGGF ...String:
MHHGTGPQNV QHQLQRSRAC PGSEGEEQPA HPNPPPSPAA PFAPSASPSA PQSPSYQIQQ LMNRSPATGQ NVNITLQSVG PVVGGNQQIT LAPLPLPSPT SPGFQFSAQP RRFEHGSPSY IQVTSPLSQQ VQTQSPTQPS PGPGQALQNV RAGAPGPGLG LCSSSPTGGF VDASVLVRQI SLSPSSGGHF VFQDGSGLTQ IAQGAQVQLQ HPGTPITVRE RRPSQPHTQS GGTIHHLGPQ SPAAAGGAGL QPLASPSHIT TANLPPQISS IIQGQLVQQQ QVLQGPPLPR PLGFERTPGV LLPGAGGAAG FGMTSPPPPT SPSRTAVPPG LSSLPLTSVG NTGMKKVPKK LEEIPPASPE MAQMRKQCLD YHYQEMQALK EVFKEYLIEL FFLQHFQGNM MDFLAFKKKH YAPLQAYLRQ NDLDIEEEEE EEEEEEEKSE VINDEVKVVT GKDGQTGTPV AIATQLPPKV SAAFSSQQQP FQQALAGSLV AGAGSTVETD LFKRQQAMPS TGMAEQSKRP RLEVGHQGVV FQHPGADAGV PLQQLMPTAQ GGMPPTPQAA QLAGQRQSQQ QYDPSTGPPV QNAASLHTPL PQLPGRLPPA GVPTAALSSA LQFAQQPQVV EAQTQLQIPV KTQQPNVPIP APPSSQLPIP PSQPAQLALH VPTPGKVQVQ ASQLSSLPQM VASTRLPVDP APPCPRPLPT SSTSSLAPVS GSGPGPSPAR SSPVNRPSSA TNKALSPVTS RTPGVVASAP TKPQSPAQNA TSSQDSSQDT LTEQITLENQ VHQRIAELRK AGLWSQRRLP KLQEAPRPKS HWDYLLEEMQ WMATDFAQER RWKVAAAKKL VRTVVRHHEE KQLREERGKK EEQSRLRRIA ASTAREIECF WSNIEQVVEI KLRVELEEKR KKALNLQKVS RRGKELRPKG FDALQESSLD SGMSGRKRKA SISLTDDEVD DEEETIEEEE ANEGVVDHQT ELSNLAKEAE LPLLDLMKLY EGAFLPSSQW PRPKPDGEDT SGEEDADDCP GDRESRKDLV LIDSLFIMDQ FKAAERMNIG KPNAKDIADV TAVAEAILPK GSARVTTSVK FNAPSLLYGA LRDYQKIGLD WLAKLYRKNL NGILADEAGL GKTVQIIAFF AHLACNEGNW GPHLVVVRSC NILKWELELK RWCPGLKILS YIGSHRELKA KRQEWAEPNS FHVCITSYTQ FFRGLTAFTR VRWKCLVIDE MQRVKGMTER HWEAVFTLQS QQRLLLIDSP LHNTFLELWT MVHFLVPGIS RPYLSSPLRA PSEESQDYYH KVVIRLHRVT QPFILRRTKR DVEKQLTKKY EHVLKCRLSN RQKALYEDVI LQPGTQEALK SGHFVNVLSI LVRLQRICNH PGLVEPRHPG SSYVAGPLEY PSASLILKAL ERDFWKEADL SMFDLIGLEN KITRHEAELL SKKKIPRKLM EEISTSAAPA ARPAAAKLKA SRLFQPVQYG QKPEGRTVAF PSTHPPRTAA PTTASAAPQG PLRGRPPIAT FSANPEAKAA AAPFQTSQAS ASAPRHQPAS ASSTAASPAH PAKLRAQTTA QASTPGQPPP QPQAPSHAAG QSALPQRLVL PSQAQARLPS GEVVKIAQLA SITGPQSRVA QPETPVTLQF QGSKFTLSHS QLRQLTAGQP LQLQGSVLQI VSAPGQPYLR APGPVVMQTV SQAGAVHGAL GSKPPAGGPS PAPLTPQVGV PGRVAVNALA VGEPGTASKP ASPIGGPTQE EKTRLLKERL DQIYLVNERR CSQAPVYGRD LLRICALPSH GRVQWRGSLD GRRGKEAGPA HSYTSSSESP SELMLTLCRC GESLQDVIDR VAFVIPPVVA APPSLRVPRP PPLYSHRMRI LRQGLREHAA PYFQQLRQTT APRLLQFPEL RLVQFDSGKL EALAILLQKL KSEGRRVLIL SQMILMLDIL EMFLNFHYLT YVRIDENASS EQRQELMRSF NRDRRIFCAI LSTHSRTTGI NLVEADTVVF YDNDLNPVMD AKAQEWCDRI GRCKDIHIYR LVSGNSIEEK LLKNGTKDLI REVAAQGNDY SMAFLTQRTI QELFEVYSPM DDAGFPVKAE EFVVLSQEPS VTETIAPKIA RPFIEALKSI EYLEEDAQKS AQEGVLGPHT DALSSDSENM PCDEEPSQLE ELADFMEQLT PIEKYALNYL ELFHTSIEQE KERNSEDAVM TAVRAWEFWN LKTLQEREAR LRLEQEEAEL LTYTREDAYS MEYVYEDVDG QTEVMPLWTP PTPPQDDSDI YLDSVMCLMY EATPIPEAKL PPVYVRKERK RHKTDPSAAG RKKKQRHGEA VVPPRSLFDR ATPGLLKIRR EGKEQKKNIL LKQQVPFAKP LPTFAKPTAE PGQDNPEWLI SEDWALLQAV KQLLELPLNL TIVSPAHTPN WDLVSDVVNS CSRIYRSSKQ CRNRYENVII PREEGKSKNN RPLRTSQIYA QDENATHTQL YTSHFDLMKM TAGKRSPPIK PLLGMNPFQK NPKHASVLAE SGINYDKPLP PIQVASLRAE RIAKEKKALA DQQKAQQPAV AQPPPPQPQP PPPPQQPPPP LPQPQAAGSQ PPAGPPAVQP QPQPQPQTQP QPVQAPAKAQ PAITTGGSAA VLAGTIKTSV TGTSMPTGAV SGNVIVNTIA GVPAATFQSI NKRLASPVAP GALTTPGGSA PAQVVHTQPP PRAVGSPATA TPDLVSMATT QGVRAVTSVT ASAVVTTNLT PVQTPARSLV PQVSQATGVQ LPGKTITPAH FQLLRQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQTTTTSQ VQVPQIQGQA QSPAQIKAVG KLTPEHLIKM QKQKLQMPPQ PPPPQAQSAP PQPTAQVQVQ TSQPPQQQSP QLTTVTAPRP GALLTGTTVA NLQVARLTRV PTSQLQAQGQ MQTQAPQPAQ VALAKPPVVS VPAAVVSSPG VTTLPMNVAG ISVAIGQPQK AAGQTVVAQP VHMQQLLKLK QQAVQQQKAI QPQAAQGPAA VQQKITAQQI TTPGAQQKVA YAAQPALKTQ FLTTPISQAQ KLAGAQQVQT QIQVAKLPQV VQQQTPVASI QQVASASQQA SPQTVALTQA TAAGQQVQMI PAVTATAQVV QQKLIQQQVV TTASAPLQTP GAPNPAQVPA SSDSPSQQPK LQMRVPAVRL KTPTKPPCQ

UniProtKB: E1A-binding protein p400

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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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
20.0 mMHEPES
250.0 mMNaCl
2.0 mMMgCL2
20.0 mMBiotin
1.0 %Trehalose
2.0 mMDTT
0.0125 %DDM
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.5 µm
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

Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 181210
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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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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