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- EMDB-45206: Reconstituted P400 Subcomplex of the human TIP60 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45206
TitleReconstituted P400 Subcomplex of the human TIP60 complex
Map data
Sample
  • Complex: Reconstituted P400 Subcomplex of the human TIP60 complex
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: Enhancer of polycomb homolog 1
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: E1A-binding protein p400
    • Protein or peptide: DNA methyltransferase 1-associated protein 1
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordscomplex / chromatin regulator / GENE REGULATION
Function / homology
Function and homology information


piccolo histone acetyltransferase complex / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / positive regulation of norepinephrine uptake / 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 / telomerase RNA localization to Cajal body / positive regulation of norepinephrine uptake / 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 / R2TP complex / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / dynein axonemal particle / morphogenesis of a polarized epithelium / neural retina development / protein localization to adherens junction / postsynaptic actin cytoskeleton / Swr1 complex / structural constituent of postsynaptic actin cytoskeleton / protein antigen binding / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / Tat protein binding / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / RPAP3/R2TP/prefoldin-like complex / chromatin-protein adaptor activity / Ino80 complex / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / apical protein localization / regulation of double-strand break repair / blastocyst formation / box C/D snoRNP assembly / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / protein folding chaperone complex / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / positive regulation of double-strand break repair / spinal cord development / maintenance of blood-brain barrier / regulation of chromosome organization / NuA4 histone acetyltransferase complex / negative regulation of gene expression, epigenetic / establishment or maintenance of cell polarity / cortical cytoskeleton / spermatid development / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / TFIID-class transcription factor complex binding / brush border / regulation of embryonic development / kinesin binding / MLL1 complex / somatic stem cell population maintenance / Telomere Extension By Telomerase / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / enzyme-substrate adaptor activity / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / regulation of protein localization to plasma membrane / RNA polymerase II core promoter sequence-specific DNA binding / DNA helicase activity / cytoskeleton organization / Deposition of new CENPA-containing nucleosomes at the centromere / EPHB-mediated forward signaling / TBP-class protein binding / substantia nigra development / calyx of Held
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 / 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 / HSA 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: 2.75 Å
AuthorsYang Z / Mameri A / Florez Ariza AJ / Cote J / Nogales E
Funding support United States, Canada, 5 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Canada Research Chairs Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR) Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2024
Title: Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex.
Authors: Zhenlin Yang / Amel Mameri / Claudia Cattoglio / Catherine Lachance / Alfredo Jose Florez Ariza / Jie Luo / Jonathan Humbert / Deepthi Sudarshan / Arul Banerjea / Maxime Galloy / Amélie ...Authors: Zhenlin Yang / Amel Mameri / Claudia Cattoglio / Catherine Lachance / Alfredo Jose Florez Ariza / Jie Luo / Jonathan Humbert / Deepthi Sudarshan / Arul Banerjea / Maxime Galloy / Amélie Fradet-Turcotte / Jean-Philippe Lambert / Jeff A Ranish / Jacques Côté / Eva Nogales /
Abstract: The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) ...The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4, H2A, and H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the E1A binding protein P400 (EP400) subunit serves as a scaffold holding the different functional modules in specific positions, creating a distinct arrangement of the actin-related protein (ARP) module. EP400 interacts with the transformation/transcription domain-associated protein (TRRAP) subunit by using a footprint that overlaps with that of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.
History
DepositionJun 5, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45206.png

Downloads & links

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Map

FileDownload / File: emd_45206.map.gz / Format: CCP4 / Size: 204.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 377 pix.
= 377. Å		1 Å/pix.
x 377 pix.
= 377. Å		1 Å/pix.
x 377 pix.
= 377. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 2.4
Minimum - Maximum-0.8212818 - 21.006815
Average (Standard dev.)0.010135023 (±0.5691748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions377377377
Spacing377377377
CellA=B=C: 377.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45206_half_map_1.map
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Half map: #1

Fileemd_45206_half_map_2.map
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Sample components

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Entire : Reconstituted P400 Subcomplex of the human TIP60 complex

EntireName: Reconstituted P400 Subcomplex of the human TIP60 complex
Components
  • Complex: Reconstituted P400 Subcomplex of the human TIP60 complex
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: Enhancer of polycomb homolog 1
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: E1A-binding protein p400
    • Protein or peptide: DNA methyltransferase 1-associated protein 1
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Reconstituted P400 Subcomplex of the human TIP60 complex

SupramoleculeName: Reconstituted P400 Subcomplex of the human 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: Enhancer of polycomb homolog 1

MacromoleculeName: Enhancer of polycomb homolog 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.589172 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 NSSTNTSQNL ASNQQKSGFR LNIQGLE RT LQGFVSKTLD SASAQFAASA LVTSEQLMGF KMKDDVVLGI GVNGVLPASG VYKGLHLSST TPTALVHTSP STAGSALL Q PSNITQTSSS HSALSHQVTA ANSATTQVLI GNNIRLTVPS SVATVNSIAP INARHIPRTL SAVPSSALKL AAAANCQVS KVPSSSSVDS VPRENHESEK PALNNIADNT VAMEVT

UniProtKB: Enhancer of polycomb homolog 1

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Macromolecule #3: Actin-like protein 6A

MacromoleculeName: Actin-like protein 6A / type: protein_or_peptide / ID: 3 / 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 #4: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 4 / 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 #5: E1A-binding protein p400

MacromoleculeName: E1A-binding protein p400 / type: protein_or_peptide / ID: 5 / 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: 343.867312 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 VKVVTGKDGQ TGTPVAIATQ LPPKVSAAFS SQQQP FQQA LAGSLVAGAG STVETDLFKR QQAMPSTGMA EQSKRPRLEV GHQGVVFQHP GADAGVPLQQ LMPTAQGGMP PTPQAA QLA GQRQSQQQYD PSTGPPVQNA ASLHTPLPQL PGRLPPAGVP TAALSSALQF AQQPQVVEAQ TQLQIPVKTQ QPNVPIP AP PSSQLPIPPS QPAQLALHVP TPGKVQVQAS QLSSLPQMVA STRLPVDPAP PCPRPLPTSS TSSLAPVSGS GPGPSPAR S SPVNRPSSAT NKALSPVTSR TPGVVASAPT KPQSPAQNAT SSQDSSQDTL TEQITLENQV HQRIAELRKA GLWSQRRLP KLQEAPRPKS HWDYLLEEMQ WMATDFAQER RWKVAAAKKL VRTVVRHHEE KQLREERGKK EEQSRLRRIA ASTAREIECF WSNIEQVVE IKLRVELEEK RKKALNLQKV SRRGKELRPK GFDALQESSL DSGMSGRKRK ASISLTDDEV DDEEETIEEE E ANEGVVDH QTELSNLAKE AELPLLDLMK LYEGAFLPSS QWPRPKPDGE DTSGEEDADD CPGDRESRKD LVLIDSLFIM DQ FKAAERM NIGKPNAKDI ADVTAVAEAI LPKGSARVTT SVKFNAPSLL YGALRDYQKI GLDWLAKLYR KNLNGILADE AGL GKTVQI IAFFAHLACN EGNWGPHLVV VRSCNILKWE LELKRWCPGL KILSYIGSHR ELKAKRQEWA EPNSFHVCIT SYTQ FFRGL TAFTRVRWKC LVIDEMQRVK GMTERHWEAV FTLQSQQRLL LIDSPLHNTF LELWTMVHFL VPGISRPYLS SPLRA PSEE SQDYYHKVVI RLHRVTQPFI LRRTKRDVEK QLTKKYEHVL KCRLSNRQKA LYEDVILQPG TQEALKSGHF VNVLSI LVR LQRICNHPGL VEPRHPGSSY VAGPLEYPSA SLILKALERD FWKEADLSMF DLIGLENKIT RHEAELLSKK KIPRKLM EE ISTSAAPAAR PAAAKLKASR LFQPVQYGQK PEGRTVAFPS THPPRTAAPT TASAAPQGPL RGRPPIATFS ANPEAKAA A APFQTSQASA SAPRHQPASA SSTAASPAHP AKLRAQTTAQ ASTPGQPPPQ PQAPSHAAGQ SALPQRLVLP SQAQARLPS GEVVKIAQLA SITGPQSRVA QPETPVTLQF QGSKFTLSHS QLRQLTAGQP LQLQGSVLQI VSAPGQPYLR APGPVVMQTV SQAGAVHGA LGSKPPAGGP SPAPLTPQVG VPGRVAVNAL AVGEPGTASK PASPIGGPTQ EEKTRLLKER LDQIYLVNER R CSQAPVYG RDLLRICALP SHGRVQWRGS LDGRRGKEAG PAHSYTSSSE SPSELMLTLC RCGESLQDVI DRVAFVIPPV VA APPSLRV PRPPPLYSHR MRILRQGLRE HAAPYFQQLR QTTAPRLLQF PELRLVQFDS GKLEALAILL QKLKSEGRRV LIL SQMILM LDILEMFLNF HYLTYVRIDE NASSEQRQEL MRSFNRDRRI FCAILSTHSR TTGINLVEAD TVVFYDNDLN PVMD AKAQE WCDRIGRCKD IHIYRLVSGN SIEEKLLKNG TKDLIREVAA QGNDYSMAFL TQRTIQELFE VYSPMDDAGF PVKAE EFVV LSQEPSVTET IAPKIARPFI EALKSIEYLE EDAQKSAQEG VLGPHTDALS SDSENMPCDE EPSQLEELAD FMEQLT PIE KYALNYLELF HTSIEQEKER NSEDAVMTAV RAWEFWNLKT LQEREARLRL EQEEAELLTY TREDAYSMEY VYEDVDG QT EVMPLWTPPT PPQDDSDIYL DSVMCLMYEA TPIPEAKLPP VYVRKERKRH KTDPSAAGRK KKQRHGEAVV PPRSLFDR A TPGLLKIRRE GKEQKKNILL KQQVPFAKPL PTFAKPTAEP GQDNPEWLIS EDWALLQAVK QLLELPLNLT IVSPAHTPN WDLVSDVVNS CSRIYRSSKQ CRNRYENVII PREEGKSKNN RPLRTSQIYA QDENATHTQL YTSHFDLMKM TAGKRSPPIK PLLGMNPFQ KNPKHASVLA ESGINYDKPL PPIQVASLRA ERIAKEKKAL ADQQKAQQPA VAQPPPPQPQ PPPPPQQPPP P LPQPQAAG SQPPAGPPAV QPQPQPQPQT QPQPVQAPAK AQPAITTGGS AAVLAGTIKT SVTGTSMPTG AVSGNVIVNT IA GVPAATF QSINKRLASP VAPGALTTPG GSAPAQVVHT QPPPRAVGSP ATATPDLVSM ATTQGVRAVT SVTASAVVTT NLT PVQTPA RSLVPQVSQA TGVQLPGKTI TPAHFQLLRQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQTT TTSQVQVPQI QGQA QSPAQ IKAVGKLTPE HLIKMQKQKL QMPPQPPPPQ AQSAPPQPTA QVQVQTSQPP QQQSPQLTTV TAPRPGALLT GTTVA NLQV ARLTRVPTSQ LQAQGQMQTQ APQPAQVALA KPPVVSVPAA VVSSPGVTTL PMNVAGISVA IGQPQKAAGQ TVVAQP VHM QQLLKLKQQA VQQQKAIQPQ AAQGPAAVQQ KITAQQITTP GAQQKVAYAA QPALKTQFLT TPISQAQKLA GAQQVQT QI QVAKLPQVVQ QQTPVASIQQ VASASQQASP QTVALTQATA AGQQVQMIPA VTATAQVVQQ KLIQQQVVTT ASAPLQTP G APNPAQVPAS SDSPSQQPKL QMRVPAVRLK TPTKPPCQ

UniProtKB: E1A-binding protein p400

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Macromolecule #6: DNA methyltransferase 1-associated protein 1

MacromoleculeName: DNA methyltransferase 1-associated protein 1 / type: protein_or_peptide / ID: 6 / 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 #7: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
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 #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: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 9 / Number of copies: 7 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: 4D-STEM / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166442
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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