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- EMDB-45389: Cryo-EM structure of the reconstituted TRRAP lobe of the human TI... -

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Basic information

Entry
Database: EMDB / ID: EMD-45389
TitleCryo-EM structure of the reconstituted TRRAP lobe of the human TIP60 complex (composite structure)
Map data
Sample
  • Complex: Reconstituted TRRAP lobe of the TIP60 complex
    • Protein or peptide: E1A-binding protein p400,Haloalkane dehalogenase chimera
    • Protein or peptide: Isoform 2 of Transformation/transcription domain-associated protein
  • Ligand: INOSITOL HEXAKISPHOSPHATE
Keywordshistone acetyltransferase / chromatin regulator / transcription regulation / GENE REGULATION
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex ...haloalkane dehalogenase / haloalkane dehalogenase activity / transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / regulation of RNA splicing / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / helicase activity / DNA Damage/Telomere Stress Induced Senescence / response to toxic substance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosome / HATs acetylate histones / chromatin organization / regulation of apoptotic process / regulation of cell cycle / hydrolase activity / Ub-specific processing proteases / 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 / membrane
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 / Haloalkane dehalogenase, subfamily 2 / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA 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 / Haloalkane dehalogenase, subfamily 2 / 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 / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Epoxide hydrolase-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / alpha/beta hydrolase fold / SANT/Myb domain / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Alpha/beta hydrolase fold-1 / Helicase conserved C-terminal domain / Armadillo-like helical / helicase superfamily c-terminal domain / Alpha/Beta hydrolase fold / 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
Haloalkane dehalogenase / E1A-binding protein p400 / Transformation/transcription domain-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsLouder RK / Park G / Patel AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60
Authors: Park G / Patel AB / Wu C / Louder RK
History
DepositionJun 17, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45389.png

Downloads & links

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Map

FileDownload / File: emd_45389.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 371.712 Å		0.73 Å/pix.
x 512 pix.
= 371.712 Å		0.73 Å/pix.
x 512 pix.
= 371.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.17795068 - 2.0993395
Average (Standard dev.)0.00095678703 (±0.021652922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 371.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Reconstituted TRRAP lobe of the TIP60 complex

EntireName: Reconstituted TRRAP lobe of the TIP60 complex
Components
  • Complex: Reconstituted TRRAP lobe of the TIP60 complex
    • Protein or peptide: E1A-binding protein p400,Haloalkane dehalogenase chimera
    • Protein or peptide: Isoform 2 of Transformation/transcription domain-associated protein
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: Reconstituted TRRAP lobe of the TIP60 complex

SupramoleculeName: Reconstituted TRRAP lobe of the TIP60 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 560 KDa

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Macromolecule #1: E1A-binding protein p400,Haloalkane dehalogenase chimera

MacromoleculeName: E1A-binding protein p400,Haloalkane dehalogenase chimera
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.783695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEQSKRPRL EVGHQGVVFQ HPGADAGVPL QQLMPTAQGG MPPTPQAAQL AGQRQSQQQY DPSTGPPVQN AASLHTPLPQ LPGRLPPAG VPTAALSSAL QFAQQPQVVE AQTQLQIPVK TQQPNVPIPA PPSSQLPIPP SQPAQLALHV PTPGKVQVQA S QLSSLPQM ...String:
MAEQSKRPRL EVGHQGVVFQ HPGADAGVPL QQLMPTAQGG MPPTPQAAQL AGQRQSQQQY DPSTGPPVQN AASLHTPLPQ LPGRLPPAG VPTAALSSAL QFAQQPQVVE AQTQLQIPVK TQQPNVPIPA PPSSQLPIPP SQPAQLALHV PTPGKVQVQA S QLSSLPQM VASTRLPVDP APPCPRPLPT SSTSSLAPVS GSGPGPSPAR SSPVNRPSSA TNKALSPVTS RTPGVVASAP TK PQSPAQN ATSSQDSSQD TLTEQITLEN QVHQRIAELR KAGLWSQRRL PKLQEAPRPK SHWDYLLEEM QWMATDFAQE RRW KVAAAK KLVRTVVRHH EEKQLREERG KKEEQSRLRR IAASTAREIE CFWSNIEQVV EIKLRVELEE KRKKALNLQK VSRR GPGSS DSENMPCDEE PSQLEELADF MEQLTPIEKY ALNYLELFHT SIEQEKERNS EDAVMTAVRA WEFWNLKTLQ EREAR LRLE QEEAELLTYT REDAYSMEYV YEDVDGQTEV MPLWTPPTPP QDDSDIYLDS VMCLMYEATP IPEAKLPPVY VRKERK RHK TDPSAAGRKK KQRHGEAVVP PRSLFDRATP GLLKIRREGK EQKKNILLKQ QVPFAKPLPT FAKPTAEPGQ DDNPEWL IS EDWALLQAVK QLLELPLNLT IVSPAHTPNW DLVSDVVNSC SRIYRSSKQC RNRYENVIIP REEKSKNNRP LLRTSQIY A QDENATHTQL YTSHFDLMKM TAGKRPPIKP LLGMNPFQKN PPKHASVLAE SGINYDKPLP PIQVASLRAE RIAKEKKAL DGSGGSGEDL YFQSGGSMAE IGTGFPFDPH YVEVLGERMH YVDVGPRDGT PVLFLHGNPT SSYVWRNIIP HVAPTHRCIA PDLIGMGKS DKPDLGYFFD DHVRFMDAFI EALGLEEVVL VIHDWGSALG FHWAKRNPER VKGIAFMEFI RPIPTWDEWP E FARETFQA FRTTDVGRKL IIDQNVFIEG TLPMGVVRPL TEVEMDHYRE PFLNPVDREP LWRFPNELPI AGEPANIVAL VE EYMDWLH QSPVPKLLFW GTPGVLIPPA EAARLAKSLP NCKAVDIGPG LNLLQEDNPD LIGSEIARWL STLEISGGGH HHH HH

UniProtKB: E1A-binding protein p400, E1A-binding protein p400, Haloalkane dehalogenase

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Macromolecule #2: Isoform 2 of Transformation/transcription domain-associated protein

MacromoleculeName: Isoform 2 of Transformation/transcription domain-associated protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 433.231312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQL RKLVLEIIHR IPTNEHLRPH TKNVLSVMFR FLETENEENV LICLRIIIEL HKQFRPPITQ EIHHFLDFVK Q IYKELPKV ...String:
MAFVATQGAT VVDQTTLMKK YLQFVAALTD VNTPDETKLK MMQEVSENFE NVTSSPQYST FLEHIIPRFL TFLQDGEVQF LQEKPAQQL RKLVLEIIHR IPTNEHLRPH TKNVLSVMFR FLETENEENV LICLRIIIEL HKQFRPPITQ EIHHFLDFVK Q IYKELPKV VNRYFENPQV IPENTVPPPE MVGMITTIAV KVNPEREDSE TRTHSIIPRG SLSLKVLAEL PIIVVLMYQL YK LNIHNVV AEFVPLIMNT IAIQVSAQAR QHKLYNKELY ADFIAAQIKT LSFLAYIIRI YQELVTKYSQ QMVKGMLQLL SNC PAETAH LRKELLIAAK HILTTELRNQ FIPCMDKLFD ESILIGSGYT ARETLRPLAY STLADLVHHV RQHLPLSDLS LAVQ LFAKN IDDESLPSSI QTMSCKLLLN LVDCIRSKSE QESGNGRDVL MRMLEVFVLK FHTIARYQLS AIFKKCKPQS ELGAV EAAL PGSGGGASGG GSGEKDKEDK QTFQVTDCRS LVKTLVCGVK TITWGITSCK APGEAQFIPN KQLQPKETQI YIKLVK YAM QALDIYQVQI AGNGQTYIRV ANCQTVRMKE EKEVLEHFAG VFTMMNPLTF KEIFQTTVPY MVERISKNYA LQIVANS FL ANPTTSALFA TILVEYLLDR LPEMGSNVEL SNLYLKLFKL VFGSVSLFAA ENEQMLKPHL HKIVNSSMEL AQTAKEPY N YFLLLRALFR SIGGGSHDLL YQEFLPLLPN LLQGLNMLQS GLHKQHMKDL FVELCLTVPV RLSSLLPYLP MLMDPLVSA LNGSQTLVSQ GLRTLELCVD NLQPDFLYDH IQPVRAELMQ ALWRTLRNPA DSISHVAYRV LGKFGGSNRK MLKESQKLHY VVTEVQGPS ITVEFSDCKA SLQLPMEKAI ETALDCLKSA NTEPYYRRQA WEVIKCFLVA MMSLEDNKHA LYQLLAHPNF T EKTIPNVI ISHRYKAQDT PARKTFEQAL TGAFMSAVIK DLRPSALPFV ASLIRHYTMV AVAQQCGPFL LPCYQVGSQP ST AMFHSEE NGSKGMDPLV LIDAIAICMA YEEKELCKIG EVALAVIFDV ASIILGSKER ACQLPLFSYI VERLCACCYE QAW YAKLGG VVSIKFLMER LPLTWVLQNQ QTFLKALLFV MMDLTGEVSN GAVAMAKTTL EQLLMRCATP LKDEERAEEI VAAQ EKSFH HVTHDLVREV TSPNSTVRKQ AMHSLQVLAQ VTGKSVTVIM EPHKEVLQDM VPPKKHLLRH QPANAQIGLM EGNTF CTTL QPRLFTMDLN VVEHKVFYTE LLNLCEAEDS ALTKLPCYKS LPSLVPLRIA ALNALAACNY LPQSREKIIA ALFKAL NST NSELQEAGEA CMRKFLEGAT IEVDQIHTHM RPLLMMLGDY RSLTLNVVNR LTSVTRLFPN SFNDKFCDQM MQHLRKW ME VVVITHKGGQ RSDGNEMKIC SAIINLFHLI PAAPQTLVKP LLEVVMKTER AMLIEAGSPF REPLIKFLTR HPSQTVEL F MMEATLNDPQ WSRMFMSFLK HKDARPLRDV LAANPNRFIT LLLPGGAQTA VRPGSPSTST MRLDLQFQAI KIISIIVKN DDSWLASQHS LVSQLRRVWV SENFQERHRK ENMAATNWKE PKLLAYCLLN YCKRNYGDIE LLFQLLRAFT GRFLCNMTFL KEYMEEEIP KNYSIAQKRA LFFRFVDFND PNFGDELKAK VLQHILNPAF LYSFEKGEGE QLLGPPNPEG DNPESITSVF I TKVLDPEK QADMLDSLRI YLLQYATLLV EHAPHHIHDN NKNRNSKLRR LMTFAWPCLL SKACVDPACK YSGHLLLAHI IA KFAIHKK IVLQVFHSLL KAHAMEARAI VRQAMAILTP AVPARMEDGH QMLTHWTRKI IVEEGHTVPQ LVHILHLIVQ HFK VYYPVR HHLVQHMVSA MQRLGFTPSV TIEQRRLAVD LSEVVIKWEL QRIKDQQPDS DMDPNSSGEG GDYKDHDIDY KDDD DKGSV SSSIKRGLSV DSAQEVKRFR TATGAISAVF GRSQSLPGAD SLLAKPIDKQ HTDTVVNFLI RVACQVNDNT NTAGS PGEV LSRRCVNLLK TALRPDMWPK SELKLQWFDK LLMTVEQPNQ VNYGNICTGL EVLSFLLTVL QSPAILSSFK PLQRGI AAC MTCGNTKVLR AVHSLLSRLM SIFPTEPSTS SVASKYEELE CLYAAVGKVI YEGLTNYEKA TNANPSQLFG TLMILKS AC SNNPSYIDRL ISVFMRSLQK MVREHLNPQA ASGSTEATSG TSELVMLSLE LVKTRLAVMS MEMRKNFIQA ILTSLIEK S PDAKILRAVV KIVEEWVKNN SPMAANQTPT LREKSILLVK MMTYIEKRFP EDLELNAQFL DLVNYVYRDE TLSGSELTA KLEPAFLSGL RCAQPLIRAK FFEVFDNSMK RRVYERLLYV TCSQNWEAMG NHFWIKQCIE LLLAVCEKST PIGTSCQGAM LPSITNVIN LADSHDRAAF AMVTHVKQEP RERENSESKE EDVEIDIELA PGDQTSTPKT KELSEKDIGN QLHMLTNRHD K FLDTLREV KTGALLSAFV QLCHISTTLA EKTWVQLFPR LWKILSDRQQ HALAGEISPF LCSGSHQVQR DCQPSALNCF VE AMSQCVP PIPIRPCVLK YLGKTHNLWF RSTLMLEHQA FEKGLSLQIK PKQTTEFYEQ ESITPPQQEI LDSLAELYSL LQE EDMWAG LWQKRCKYSE TATAIAYEQH GFFEQAQESY EKAMDKAKKE HERSNASPAI FPEYQLWEDH WIRCSKELNQ WEAL TEYGQ SKGHINPYLV LECAWRVSNW TAMKEALVQV EVSCPKEMAW KVNMYRGYLA ICHPEEQQLS FIERLVEMAS SLAIR EWRR LPHVVSHVHT PLLQAAQQII ELQEAAQINA GLQPTNLGRN NSLHDMKTVV KTWRNRLPIV SDDLSHWSSI FMWRQH HYQ AIVTAYENSS QHDPSSNNAM LGVHASASAI IQYGKIARKQ GLVNVALDIL SRIHTIPTVP IVDCFQKIRQ QVKCYLQ LA GVMGKNECMQ GLEVIESTNL KYFTKEMTAE FYALKGMFLA QINKSEEANK AFSAAVQMHD VLVKAWAMWG DYLENIFV K ERQLHLGVSA ITCYLHACRH QNESKSRKYL AKVLWLLSFD DDKNTLADAV DKYCIGVPPI QWLAWIPQLL TCLVGSEGK LLLNLISQVG RVYPQAVYFP IRTLYLTLKI EQRERYKSDP GPIRATAPMW RCSRIMHMQR ELHPTLLSSL EGIVDQMVWF RENWHEEVL RQLQQGLAKC YSVAFEKSGA VSDAKITPHT LNFVKKLVST FGVGLENVSN VSTMFSSAAS ESLARRAQAT A QDPVFQKL KGQFTTDFDF SVPGSMKLHN LISKLKKWIK ILEAKTKQLP KFFLIEEKCR FLSNFSAQTA EVEIPGEFLM PK PTHYYIK IARFMPRVEI VQKHNTAARR LYIRGHNGKI YPYLVMNDAC LTESRREERV LQLLRLLNPC LEKRKETTKR HLF FTVPRV VAVSPQMRLV EDNPSSLSLV EIYKQRCAKK GIEHDNPISR YYDRLATVQA RGTQASHQVL RDILKEVQSN MVPR SMLKE WALHTFPNAT DYWTFRKMFT IQLALIGFAE FVLHLNRLNP EMLQIAQDTG KLNVAYFRFD INDATGDLDA NRPVP FRLT PNISEFLTTI GVSGPLTASM IAVARCFAQP NFKVDGILKT VLRDEIIAWH KKTQEDTSSP LSAAGQPENM DSQQLV SLV QKAVTAIMTR LHNLAQFEGG ESKVNTLVAA ANSLDNLCRM DPAWHPWL

UniProtKB: Transformation/transcription domain-associated protein

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Macromolecule #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 141352
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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