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- EMDB-38718: The core subcomplex of human NuA4/TIP60 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38718
TitleThe core subcomplex of human NuA4/TIP60 complex
Map dataThe core subcomplex of human TIP60 complex
Sample
  • Complex: The core subcomplex of human NuA4/TIP60 complex
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: DNA methyltransferase 1-associated protein 1
    • Protein or peptide: Isoform 2 of E1A-binding protein p400
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Isoform 2 of Enhancer of polycomb homolog 1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsRemodeler / Histone Acetyltransferase Complex / NuA4 / TIP60 / TRANSCRIPTION
Function / homology
Function and homology information


piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / sperm DNA condensation / histone chaperone activity / establishment of protein localization to chromatin / cellular response to cytochalasin B ...piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / positive regulation of norepinephrine uptake / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / sperm DNA condensation / histone chaperone activity / establishment of protein localization to chromatin / cellular response to cytochalasin B / bBAF complex / npBAF complex / R2TP complex / nBAF complex / brahma complex / regulation of transepithelial transport / dynein axonemal particle / neural retina development / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / protein localization to adherens junction / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Swr1 complex / dense body / Cell-extracellular matrix interactions / postsynaptic actin cytoskeleton / Tat protein binding / RPAP3/R2TP/prefoldin-like complex / protein antigen binding / chromatin-protein adaptor activity / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / Ino80 complex / blastocyst formation / regulation of nucleotide-excision repair / regulation of double-strand break repair / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / tight junction / box C/D snoRNP assembly / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / protein folding chaperone complex / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / regulation of norepinephrine uptake / apical junction complex / transporter regulator activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / positive regulation of double-strand break repair / spinal cord development / maintenance of blood-brain barrier / nitric-oxide synthase binding / negative regulation of gene expression, epigenetic / establishment or maintenance of cell polarity / cortical cytoskeleton / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle / TFIID-class transcription factor complex binding / regulation of DNA replication / MLL1 complex / kinesin binding / regulation of embryonic development / Telomere Extension By Telomerase / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / somatic stem cell population maintenance / spermatid development / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / enzyme-substrate adaptor activity / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / cytoskeleton organization / EPHB-mediated forward signaling / Deposition of new CENPA-containing nucleosomes at the centromere / substantia nigra development / telomere maintenance / axonogenesis / DNA helicase activity
Similarity search - Function
Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Enhancer of polycomb protein ...Enhancer of polycomb, C-terminal / Enhancer of Polycomb C-terminus / DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Enhancer of polycomb protein / Vps72/YL1, N-terminal / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Helicase/SANT-associated domain / HSA domain profile. / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT/Myb domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Actin-like protein 6A / Actin, cytoplasmic 1 / Vacuolar protein sorting-associated protein 72 homolog / E1A-binding protein p400 / Enhancer of polycomb homolog 1 / DNA methyltransferase 1-associated protein 1 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen K / Wang L / Yu Z / Yu J / Ren Y / Wang Q / Xu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the human TIP60 complex.
Authors: Ke Chen / Li Wang / Zishuo Yu / Jiali Yu / Yulei Ren / Qianmin Wang / Yanhui Xu /
Abstract: Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell ...Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell cycle control, and embryonic development. Here we report the cryo-electron microscopy structures of the human TIP60 complex with the core subcomplex and TRRAP module refined to 3.2-Å resolution. The structures show that EP400 acts as a backbone integrating the motor module, the ARP module, and the TRRAP module. The RUVBL1-RUVBL2 hexamer serves as a rigid core for the assembly of EP400 ATPase and YL1 in the motor module. In the ARP module, an ACTL6A-ACTB heterodimer and an extra ACTL6A make hydrophobic contacts with EP400 HSA helix, buttressed by network interactions among DMAP1, EPC1, and EP400. The ARP module stably associates with the motor module but is flexibly tethered to the TRRAP module, exhibiting a unique feature of human TIP60. The architecture of the nucleosome-bound human TIP60 reveals an unengaged nucleosome that is located between the core subcomplex and the TRRAP module. Our work illustrates the molecular architecture of human TIP60 and provides architectural insights into how this complex is bound by the nucleosome.
History
DepositionJan 15, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38718.png

Downloads & links

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Map

FileDownload / File: emd_38718.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe core subcomplex of human TIP60 complex
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 300 pix.
= 400.2 Å		1.33 Å/pix.
x 300 pix.
= 400.2 Å		1.33 Å/pix.
x 300 pix.
= 400.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.334 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.12466709 - 0.25158393
Average (Standard dev.)0.0003176818 (±0.007099864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 400.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The actin-related module of human TIP60 complex

Fileemd_38718_additional_1.map
AnnotationThe actin-related module of human TIP60 complex
Projections & Slices
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Half map: Human TIP60 core subcomplex half map2

Fileemd_38718_half_map_1.map
AnnotationHuman TIP60 core subcomplex half map2
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Half map: Human TIP60 core subcomplex half map1

Fileemd_38718_half_map_2.map
AnnotationHuman TIP60 core subcomplex half map1
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Sample components

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Entire : The core subcomplex of human NuA4/TIP60 complex

EntireName: The core subcomplex of human NuA4/TIP60 complex
Components
  • Complex: The core subcomplex of human NuA4/TIP60 complex
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: DNA methyltransferase 1-associated protein 1
    • Protein or peptide: Isoform 2 of E1A-binding protein p400
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Isoform 2 of Enhancer of polycomb homolog 1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: The core subcomplex of human NuA4/TIP60 complex

SupramoleculeName: The core subcomplex of human NuA4/TIP60 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.296914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

UniProtKB: RuvB-like 1

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.222465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTS

UniProtKB: RuvB-like 2

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Macromolecule #3: DNA methyltransferase 1-associated protein 1

MacromoleculeName: DNA methyltransferase 1-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.090699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATGADVRDI LELGGPEGDA ASGTISKKDI INPDKKKSKK SSETLTFKRP EGMHREVYAL LYSDKKDAPP LLPSDTGQGY RTVKAKLGS KKVRPWKWMP FTNPARKDGA MFFHWRRAAE EGKDYPFARF NKTVQVPVYS EQEYQLYLHD DAWTKAETDH L FDLSRRFD ...String:
MATGADVRDI LELGGPEGDA ASGTISKKDI INPDKKKSKK SSETLTFKRP EGMHREVYAL LYSDKKDAPP LLPSDTGQGY RTVKAKLGS KKVRPWKWMP FTNPARKDGA MFFHWRRAAE EGKDYPFARF NKTVQVPVYS EQEYQLYLHD DAWTKAETDH L FDLSRRFD LRFVVIHDRY DHQQFKKRSV EDLKERYYHI CAKLANVRAV PGTDLKIPVF DAGHERRRKE QLERLYNRTP EQ VAEEEYL LQELRKIEAR KKEREKRSQD LQKLITAADT TAEQRRTERK APKKKLPQKK EAEKPAVPET AGIKFPDFKS AGV TLRSQR MKLPSSVGQK KIKALEQMLL ELGVELSPTP TEELVHMFNE LRSDLVLLYE LKQACANCEY ELQMLRHRHE ALAR AGVLG GPATPASGPG PASAEPAVTE PGLGPDPKDT IIDVVGAPLT PNSRKRRESA SSSSSVKKAK KP

UniProtKB: DNA methyltransferase 1-associated protein 1

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Macromolecule #4: Isoform 2 of E1A-binding protein p400

MacromoleculeName: Isoform 2 of E1A-binding protein p400 / type: protein_or_peptide / ID: 4 / 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: 340.198062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHGTGPQNV QHQLQRSRAC PGSEGEEQPA HPNPPPSPAA PFAPSASPSA PQSPSYQIQQ LMNRSPATGQ NVNITLQSVG PVVGGNQQI TLAPLPLPSP TSPGFQFSAQ PRRFEHGSPS YIQVTSPLSQ QVQTQSPTQP SPGPGQALQN VRAGAPGPGL G LCSSSPTG ...String:
MHHGTGPQNV QHQLQRSRAC PGSEGEEQPA HPNPPPSPAA PFAPSASPSA PQSPSYQIQQ LMNRSPATGQ NVNITLQSVG PVVGGNQQI TLAPLPLPSP TSPGFQFSAQ PRRFEHGSPS YIQVTSPLSQ QVQTQSPTQP SPGPGQALQN VRAGAPGPGL G LCSSSPTG GFVDASVLVR QISLSPSSGG HFVFQDGSGL TQIAQGAQVQ LQHPGTPITV RERRPSQPHT QSGGTIHHLG PQ SPAAAGG AGLQPLASPS HITTANLPPQ ISSIIQGQLV QQQQVLQGPP LPRPLGFERT PGVLLPGAGG AAGFGMTSPP PPT SPSRTA VPPGLSSLPL TSVGNTGMKK VPKKLEEIPP ASPEMAQMRK QCLDYHYQEM QALKEVFKEY LIELFFLQHF QGNM MDFLA FKKKHYAPLQ AYLRQNDLDI EEEEEEEEEE EEKSEVINDE QQALAGSLVA GAGSTVETDL FKRQQAMPST GMAEQ SKRP RLEVGHQGVV FQHPGADAGV PLQQLMPTAQ GGMPPTPQAA QLAGQRQSQQ QYDPSTGPPV QNAASLHTPL PQLPGR LPP AGVPTAALSS ALQFAQQPQV VEAQTQLQIP VKTQQPNVPI PAPPSSQLPI PPSQPAQLAL HVPTPGKVQV QASQLSS LP QMVASTRLPV DPAPPCPRPL PTSSTSSLAP VSGSGPGPSP ARSSPVNRPS SATNKALSPV TSRTPGVVAS APTKPQSP A QNATSSQDSS QDTLTEQITL ENQVHQRIAE LRKAGLWSQR RLPKLQEAPR PKSHWDYLLE EMQWMATDFA QERRWKVAA AKKLVRTVVR HHEEKQLREE RGKKEEQSRL RRIAASTARE IECFWSNIEQ VVEIKLRVEL EEKRKKALNL QKVSRRGKEL RPKGFDALQ ESSLDSGMSG RKRKASISLT DDEVDDEEET IEEEEANEGV VDHQTELSNL AKEAELPLLD LMKLYEGAFL P SSQWPRPK PDGEDTSGEE DADDCPGDRE SRKDLVLIDS LFIMDQFKAA ERMNIGKPNA KDIADVTAVA EAILPKGSAR VT TSVKFNA PSLLYGALRD YQKIGLDWLA KLYRKNLNGI LADEAGLGKT VQIIAFFAHL ACNEGNWGPH LVVVRSCNIL KWE LELKRW CPGLKILSYI GSHRELKAKR QEWAEPNSFH VCITSYTQFF RGLTAFTRVR WKCLVIDEMQ RVKGMTERHW EAVF TLQSQ QRLLLIDSPL HNTFLELWTM VHFLVPGISR PYLSSPLRAP SEESQDYYHK VVIRLHRVTQ PFILRRTKRD VEKQL TKKY EHVLKCRLSN RQKALYEDVI LQPGTQEALK SGHFVNVLSI LVRLQRICNH PGLVEPRHPG SSYVAGPLEY PSASLI LKA LERDFWKEAD LSMFDLIGLE NKITRHEAEL LSKKKIPRKL MEEISTSAAP AARPAAAKLK ASRLFQPVQY GQKPEGR TV AFPSTHPPRT AAPTTASAAP QGPLRGRPPI ATFSANPEAK AAAAPFQTSQ ASASAPRHQP ASASSTAASP AHPAKLRA Q TTAQASTPGQ PPPQPQAPSH AAGQSALPQR LVLPSQAQAR LPSGEVVKIA QLASITGPQS RVAQPETPVT LQFQGSKFT LSHSQLRQLT AGQPLQLQGS VLQIVSAPGQ PYLRAPGPVV MQTVSQAGAV HGALGSKPPA GGPSPAPLTP QVGVPGRVAV NALAVGEPG TASKPASPIG GPTQEEKTRL LKERLDQIYL VNERRCSQAP VYGRDLLRIC ALPSHGRVQW RGSLDGRRGK E AGPAHSYT SSSESPSELM LTLCRCGESL QDVIDRVAFV IPPVVAAPPS LRVPRPPPLY SHRMRILRQG LREHAAPYFQ QL RQTTAPR LLQFPELRLV QFDSGKLEAL AILLQKLKSE GRRVLILSQM ILMLDILEMF LNFHYLTYVR IDENASSEQR QEL MRSFNR DRRIFCAILS THSRTTGINL VEADTVVFYD NDLNPVMDAK AQEWCDRIGR CKDIHIYRLV SGNSIEEKLL KNGT KDLIR EVAAQGNDYS MAFLTQRTIQ ELFEVYSPMD DAGFPVKAEE FVVLSQEPSV TETIAPKIAR PFIEALKSIE YLEED AQKS AQEGVLGPHT DALSSDSENM PCDEEPSQLE ELADFMEQLT PIEKYALNYL ELFHTSIEQE KERNSEDAVM TAVRAW EFW NLKTLQEREA RLRLEQEEAE LLTYTREDAY SMEYVYEDVD GQTEVMPLWT PPTPPQDDSD IYLDSVMCLM YEATPIP EA KLPPVYVRKE RKRHKTDPSA AGRKKKQRHG EAVVPPRSLF DRATPGLLKI RREGKEQKKN ILLKQQVPFA KPLPTFAK P TAEPGQDNPE WLISEDWALL QAVKQLLELP LNLTIVSPAH TPNWDLVSDV VNSCSRIYRS SKQCRNRYEN VIIPREEGK SKNNRPLRTS QIYAQDENAT HTQLYTSHFD LMKMTAGKRS PPIKPLLGMN PFQKNPKHAS VLAESGINYD KPLPPIQVAS LRAERIAKE KKALADQQKA QQPAVAQPPP PQPQPPPPPQ QPPPPLPQPQ AAGSQPPAGP PAVQPQPQPQ PQTQPQPVQA P AKAQPAIT TGGSAAVLAG TIKTSVTGTS MPTGAVSGNV IVNTIAGVPA ATFQSINKRL ASPVAPGALT TPGGSAPAQV VH TQPPPRA VGSPATATPD LVSMATTQGV RAVTSVTASA VVTTNLTPVQ TPARSLVPQV SQATGVQLPG KTITPAHFQL LRQ QQQQQQ QQQQQQQQQQ QQQQQQQQQQ QQTTTTSQVQ VPQIQGQAQS PAQIKAVGKL TPEHLIKMQK QKLQMPPQPP PPQA QSAPP QPTAQVQVQT SQPPQQQSPQ LTTVTAPRPG ALLTGTTVAN LQVARLTRVP TSQLQAQGQM QTQAPQPAQV ALAKP PVVS VPAAVVSSPG VTTLPMNVAG ISVAIGQPQK AAGQTVVAQP VHMQQLLKLK QQAVQQQKAI QPQAAQGPAA VQQKIT AQQ ITTPGAQQKV AYAAQPALKT QFLTTPISQA QKLAGAQQVQ TQIQVAKLPQ VVQQQTPVAS IQQVASASQQ ASPQTVA LT QATAAGQQVQ MIPAVTATAQ VVQQKLIQQQ VVTTASAPLQ TPGAPNPAQV PASSDSPSQQ PKLQMRVPAV RLKTPTKP P CQ

UniProtKB: E1A-binding protein p400

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Macromolecule #5: Actin-like protein 6A

MacromoleculeName: Actin-like protein 6A / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.509812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLK NGMVEDWDSF QAILDHTYKM HVKSEASLHP VLMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA F ANGRSTGL ...String:
MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLK NGMVEDWDSF QAILDHTYKM HVKSEASLHP VLMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA F ANGRSTGL ILDSGATHTT AIPVHDGYVL QQGIVKSPLA GDFITMQCRE LFQEMNIELV PPYMIASKEA VREGSPANWK RK EKLPQVT RSWHNYMCNC VIQDFQASVL QVSDSTYDEQ VAAQMPTVHY EFPNGYNCDF GAERLKIPEG LFDPSNVKGL SGN TMLGVS HVVTTSVGMC DIDIRPGLYG SVIVAGGNTL IQSFTDRLNR ELSQKTPPSM RLKLIANNTT VERRFSSWIG GSIL ASLGT FQQMWISKQE YEEGGKQCVE RKCP

UniProtKB: Actin-like protein 6A

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Macromolecule #6: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 6 / 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: 41.78266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #7: Isoform 2 of Enhancer of polycomb homolog 1

MacromoleculeName: Isoform 2 of Enhancer of polycomb homolog 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.988273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKLSFRARA LDASKPLPVF RCEDLPDLHE YASINRAVPQ MPTGMEKEEE SEHHLQRAIS AQQVYGEKRD NMVIPVPEAE SNIAYYESI YPGEFKMPKQ LIHIQPFSLD AEQPDYDLDS EDEVFVNKLK KKMDICPLQF EEMIDRLEKG SGQQPVSLQE A KLLLKEDD ...String:
MSKLSFRARA LDASKPLPVF RCEDLPDLHE YASINRAVPQ MPTGMEKEEE SEHHLQRAIS AQQVYGEKRD NMVIPVPEAE SNIAYYESI YPGEFKMPKQ LIHIQPFSLD AEQPDYDLDS EDEVFVNKLK KKMDICPLQF EEMIDRLEKG SGQQPVSLQE A KLLLKEDD ELIREVYEYW IKKRKNCRGP SLIPSVKQEK RDGSSTNDPY VAFRRRTEKM QTRKNRKNDE ASYEKMLKLR RD LSRAVTI LEMIKRREKS KRELLHLTLE IMEKRYNLGD YNGEIMSEVM AQRQPMKPTY AIPIIPITNS SQFKHQEAMD VKE FKVNKQ DKADLIRPKR KYEKKPKVLP SSAAATPQQT SPAALPVFNA KDLNQYDFPS SDEEPLSQVL SGSSEAEEDN DPDG PFAFR RKAGCQYYAP HLDQTGNWPW TSPKDGGLGD VRYRYCLTTL TVPQRCIGFA RRRVGRGGRV LLDRAHSDYD SVFHH LDLE MLSSPQHSPV NQFANTSETN TSDKSFSKDL SQILVNIKSC RWRHFRPRTP SLHDSDNDEL SCRKLYRSIN RTGTAQ PGT QTCSTSTQSK SSSGSAHFAF TAEQYQQHQQ QLALMQKQQL AQIQQQQANS NSSTNTSQGF VSKTLDSASA QFAASAL VT SEQLMGFKMK DDVVLGIGVN GVLPASGVYK GLHLSSTTPT ALVHTSPSTA GSALLQPSNI TQTSSSHSAL SHQVTAAN S ATTQVLIGNN IRLTVPSSVA TVNSIAPINA RHIPRTLSAV PSSALKLAAA ANCQVSKVPS SSSVDSVPRE NHESEKPAL NNIADNTVAM EVT

UniProtKB: Enhancer of polycomb homolog 1

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Macromolecule #8: Vacuolar protein sorting-associated protein 72 homolog

MacromoleculeName: Vacuolar protein sorting-associated protein 72 homolog
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.658363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAY KEPLKSLRPR KVNTPAGSSQ KAREEKALLP LELQDDGSDS RKSMRQSTAE HTRQTFLRVQ ERQGQSRRRK G PHCERPLT ...String:
MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAY KEPLKSLRPR KVNTPAGSSQ KAREEKALLP LELQDDGSDS RKSMRQSTAE HTRQTFLRVQ ERQGQSRRRK G PHCERPLT QEELLREAKI TEELNLRSLE TYERLEADKK KQVHKKRKCP GPIITYHSVT VPLVGEPGPK EENVDIEGLD PA PSVSALT PHAGTGPVNP PARCSRTFIT FSDDATFEEW FPQGRPPKVP VREVCPVTHR PALYRDPVTD IPYATARAFK IIR EAYKKY ITAHGLPPTA SALGPGPPPP EPLPGSGPRA LRQKIVIK

UniProtKB: Vacuolar protein sorting-associated protein 72 homolog

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 9 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6igm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 701594
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6igm


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8xvt:
The core subcomplex of human NuA4/TIP60 complex

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