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- EMDB-18794: Human Tip60 complex with bound H2A.Z/H2B -

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Basic information

Entry
Database: EMDB / ID: EMD-18794
TitleHuman Tip60 complex with bound H2A.Z/H2B
Map dataHuman Tip60
Sample
  • Complex: Tip60 complex
    • Protein or peptide: EP400
    • Protein or peptide: EPC1
    • Protein or peptide: YL1/VPS72
    • Protein or peptide: DMAP1
    • Protein or peptide: ACL6A
    • Protein or peptide: ACTIN
    • Protein or peptide: RUVBL1
    • Protein or peptide: RUVBL2
    • Protein or peptide: H2A.Z
    • Protein or peptide: H2B
KeywordsEukaryotic transcription / Histone acetyltransferase / chromatin remodeling / Complex / 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 / bBAF complex ...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 / bBAF complex / cellular response to cytochalasin B / npBAF complex / R2TP complex / nBAF complex / brahma complex / dynein axonemal particle / neural retina development / regulation of transepithelial transport / GBAF complex / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Swr1 complex / Cell-extracellular matrix interactions / protein localization to adherens junction / dense body / RPAP3/R2TP/prefoldin-like complex / postsynaptic actin cytoskeleton / Tat protein binding / protein antigen binding / chromatin-protein adaptor activity / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / Ino80 complex / regulation of nucleotide-excision repair / regulation of double-strand break repair / blastocyst formation / RHOF GTPase cycle / Adherens junctions interactions / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / box C/D snoRNP assembly / Interaction between L1 and Ankyrins / SWI/SNF complex / tight junction / 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 / nucleosomal DNA binding / apical junction complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / positive regulation of double-strand break repair / regulation of norepinephrine uptake / transporter regulator activity / maintenance of blood-brain barrier / spinal cord development / negative regulation of gene expression, epigenetic / nitric-oxide synthase binding / cortical cytoskeleton / establishment or maintenance of cell polarity / regulation of chromosome organization / NuA4 histone acetyltransferase complex / 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 / TFIID-class transcription factor complex binding / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / MLL1 complex / regulation of embryonic development / kinesin binding / Telomere Extension By Telomerase / negative regulation of cell differentiation / EPH-ephrin mediated repulsion of cells / somatic stem cell population maintenance / spermatid development / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / enzyme-substrate adaptor activity / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / heterochromatin / regulation of DNA repair / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / EPHB-mediated forward signaling
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 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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 / Histone H2A.Z / Histone H2B type 1-B / 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: 6.2 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 31, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18794.png

Downloads & links

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Map

FileDownload / File: emd_18794.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Tip60
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 256 pix.
= 482.714 Å		1.89 Å/pix.
x 256 pix.
= 482.714 Å		1.89 Å/pix.
x 256 pix.
= 482.714 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8856 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-1.177981 - 2.8395903
Average (Standard dev.)0.0219057 (±0.11529106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 482.7136 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18794_msk_1.map
Projections & Slices
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Half map: Half map B

Fileemd_18794_half_map_1.map
AnnotationHalf map B
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Half map: Half map A

Fileemd_18794_half_map_2.map
AnnotationHalf map A
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Sample components

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Entire : Tip60 complex

EntireName: Tip60 complex
Components
  • Complex: Tip60 complex
    • Protein or peptide: EP400
    • Protein or peptide: EPC1
    • Protein or peptide: YL1/VPS72
    • Protein or peptide: DMAP1
    • Protein or peptide: ACL6A
    • Protein or peptide: ACTIN
    • Protein or peptide: RUVBL1
    • Protein or peptide: RUVBL2
    • Protein or peptide: H2A.Z
    • Protein or peptide: H2B

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Supramolecule #1: Tip60 complex

SupramoleculeName: Tip60 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: EP400

MacromoleculeName: EP400 / type: protein_or_peptide / ID: 1 / 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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Macromolecule #2: EPC1

MacromoleculeName: EPC1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSKLSFRARA LDASKPLPVF RCEDLPDLHE YASINRAVPQ MPTGMEKEEE SEHHLQRAIS AQQVYGEKRD NMVIPVPEAE SNIAYYESIY PGEFKMPKQL IHIQPFSLDA EQPDYDLDSE DEVFVNKLKK KMDICPLQFE EMIDRLEKGS GQQPVSLQEA KLLLKEDDEL ...String:
MSKLSFRARA LDASKPLPVF RCEDLPDLHE YASINRAVPQ MPTGMEKEEE SEHHLQRAIS AQQVYGEKRD NMVIPVPEAE SNIAYYESIY PGEFKMPKQL IHIQPFSLDA EQPDYDLDSE DEVFVNKLKK KMDICPLQFE EMIDRLEKGS GQQPVSLQEA KLLLKEDDEL IREVYEYWIK KRKNCRGPSL IPSVKQEKRD GSSTNDPYVA FRRRTEKMQT RKNRKNDEAS YEKMLKLRRD LSRAVTILEM IKRREKSKRE LLHLTLEIME KRYNLGDYNG EIMSEVMAQR QPMKPTYAIP IIPITNSSQF KHQEAMDVKE FKVNKQDKAD LIRPKRKYEK KPKVLPSSAA ATPQQTSPAA LPVFNAKDLN QYDFPSSDEE PLSQVLSGSS EAEEDNDPDG PFAFRRKAGC QYYAPHLDQT GNWPWTSPKD GGLGDVRYRY CLTTLTVPQR CIGFARRRVG RGGRVLLDRA HSDYDSVFHH LDLEMLSSPQ HSPVNQFANT SETNTSDKSF SKDLSQILVN IKSCRWRHFR PRTPSLHDSD NDELSCRKLY RSINRTGTAQ PGTQTCSTST QSKSSSGSAH FAFTAEQYQQ HQQQLALMQK QQLAQIQQQQ ANSNSSTNTS QNLASNQQKS GFRLNIQGLE RTLQGFVSKT LDSASAQFAA SALVTSEQLM GFKMKDDVVL GIGVNGVLPA SGVYKGLHLS STTPTALVHT SPSTAGSALL QPSNITQTSS SHSALSHQVT AANSATTQVL IGNNIRLTVP SSVATVNSIA PINARHIPRT LSAVPSSALK LAAAANCQVS KVPSSSSVDS VPRENHESEK PALNNIADNT VAMEVT

UniProtKB: Enhancer of polycomb homolog 1

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Macromolecule #3: YL1/VPS72

MacromoleculeName: YL1/VPS72 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAYK EPLKSLRPRK VNTPAGSSQK AREEKALLPL ELQDDGSDSR KSMRQSTAEH TRQTFLRVQE RQGQSRRRKG PHCERPLTQE ...String:
MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAYK EPLKSLRPRK VNTPAGSSQK AREEKALLPL ELQDDGSDSR KSMRQSTAEH TRQTFLRVQE RQGQSRRRKG PHCERPLTQE ELLREAKITE ELNLRSLETY ERLEADKKKQ VHKKRKCPGP IITYHSVTVP LVGEPGPKEE NVDIEGLDPA PSVSALTPHA GTGPVNPPAR CSRTFITFSD DATFEEWFPQ GRPPKVPVRE VCPVTHRPAL YRDPVTDIPY ATARAFKIIR EAYKKYITAH GLPPTASALG PGPPPPEPLP GSGPRALRQK IVIK

UniProtKB: Vacuolar protein sorting-associated protein 72 homolog

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Macromolecule #4: DMAP1

MacromoleculeName: DMAP1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MATGADVRDI LELGGPEGDA ASGTISKKDI INPDKKKSKK SSETLTFKRP EGMHREVYAL LYSDKKDAPP LLPSDTGQGY RTVKAKLGSK KVRPWKWMPF TNPARKDGAM FFHWRRAAEE GKDYPFARFN KTVQVPVYSE QEYQLYLHDD AWTKAETDHL FDLSRRFDLR ...String:
MATGADVRDI LELGGPEGDA ASGTISKKDI INPDKKKSKK SSETLTFKRP EGMHREVYAL LYSDKKDAPP LLPSDTGQGY RTVKAKLGSK KVRPWKWMPF TNPARKDGAM FFHWRRAAEE GKDYPFARFN KTVQVPVYSE QEYQLYLHDD AWTKAETDHL FDLSRRFDLR FVVIHDRYDH QQFKKRSVED LKERYYHICA KLANVRAVPG TDLKIPVFDA GHERRRKEQL ERLYNRTPEQ VAEEEYLLQE LRKIEARKKE REKRSQDLQK LITAADTTAE QRRTERKAPK KKLPQKKEAE KPAVPETAGI KFPDFKSAGV TLRSQRMKLP SSVGQKKIKA LEQMLLELGV ELSPTPTEEL VHMFNELRSD LVLLYELKQA CANCEYELQM LRHRHEALAR AGVLGGPATP ASGPGPASAE PAVTEPGLGP DPKDTIIDVV GAPLTPNSRK RRESASSSSS VKKAKKP

UniProtKB: DNA methyltransferase 1-associated protein 1

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Macromolecule #5: ACL6A

MacromoleculeName: ACL6A / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLKN GMVEDWDSFQ AILDHTYKMH VKSEASLHPV LMSEAPWNTR AKREKLTELM FEHYNIPAFF LCKTAVLTAF ANGRSTGLIL ...String:
MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLKN GMVEDWDSFQ AILDHTYKMH VKSEASLHPV LMSEAPWNTR AKREKLTELM FEHYNIPAFF LCKTAVLTAF ANGRSTGLIL DSGATHTTAI PVHDGYVLQQ GIVKSPLAGD FITMQCRELF QEMNIELVPP YMIASKEAVR EGSPANWKRK EKLPQVTRSW HNYMCNCVIQ DFQASVLQVS DSTYDEQVAA QMPTVHYEFP NGYNCDFGAE RLKIPEGLFD PSNVKGLSGN TMLGVSHVVT TSVGMCDIDI RPGLYGSVIV AGGNTLIQSF TDRLNRELSQ KTPPSMRLKL IANNTTVERR FSSWIGGSIL ASLGTFQQMW ISKQEYEEGG KQCVERKCP

UniProtKB: Actin-like protein 6A

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Macromolecule #6: ACTIN

MacromoleculeName: ACTIN / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA LPHAILRLDL AGRDLTDYLM KILTERGYSF TTTAEREIVR DIKEKLCYVA LDFEQEMATA ASSSSLEKSY ELPDGQVITI GNERFRCPEA LFQPSFLGME SCGIHETTFN SIMKCDVDIR KDLYANTVLS GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ EYDESGPSIV HRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #7: RUVBL1

MacromoleculeName: RUVBL1 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGSK VPFCPMVGSE VYSTEIKKTE VLMENFRRAI GLRIKETKEV YEGEVTELTP CETENPMGGY GKTISHVIIG LKTAKGTKQL ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGSK VPFCPMVGSE VYSTEIKKTE VLMENFRRAI GLRIKETKEV YEGEVTELTP CETENPMGGY GKTISHVIIG LKTAKGTKQL KLDPSIFESL QKERVEAGDV IYIEANSGAV KRQGRCDTYA TEFDLEAEEY VPLPKGDVHK KKEIIQDVTL HDLDVANARP QGGQDILSMM GQLMKPKKTE ITDKLRGEIN KVVNKYIDQG IAELVPGVLF VDEVHMLDIE CFTYLHRALE SSIAPIVIFA SNRGNCVIRG TEDITSPHGI PLDLLDRVMI IRTMLYTPQE MKQIIKIRAQ TEGINISEEA LNHLGEIGTK TTLRYSVQLL TPANLLAKIN GKDSIEKEHV EEISELFYDA KSSAKILADQ QDKYMK

UniProtKB: RuvB-like 1

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Macromolecule #8: RUVBL2

MacromoleculeName: RUVBL2 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMGM AQALGPDTPF TAIAGSEIFS LEMSKTEALT QAFRRSIGVR IKEETEIIEG EVVEIQIDRP ATGTGSKVGK LTLKTTEMET ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMGM AQALGPDTPF TAIAGSEIFS LEMSKTEALT QAFRRSIGVR IKEETEIIEG EVVEIQIDRP ATGTGSKVGK LTLKTTEMET IYDLGTKMIE SLTKDKVQAG DVITIDKATG KISKLGRSFT RARDYDAMGS QTKFVQCPDG ELQKRKEVVH TVSLHEIDVI NSRTQGFLAL FSGDTGEIKS EVREQINAKV AEWREEGKAE IIPGVLFIDE VHMLDIESFS FLNRALESDM APVLIMATNR GITRIRGTSY QSPHGIPIDL LDRLLIVSTT PYSEKDTKQI LRIRCEEEDV EMSEDAYTVL TRIGLETSLR YAIQLITAAS LVCRKRKGTE VQVDDIKRVY SLFLDESRST QYMKEYQDAF LFNELKGETM DTS

UniProtKB: RuvB-like 2

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Macromolecule #9: H2A.Z

MacromoleculeName: H2A.Z / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MAGGKAGKDS GKAKTKAVSR SQRAGLQFPV GRIHRHLKSR TTSHGRVGAT AAVYSAAILE YLTAEVLELA GNASKDLKVK RITPRHLQLA IRGDEELDSL IKATIAGGGV IPHIHKSLIG KKGQQKTV

UniProtKB: Histone H2A.Z

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Macromolecule #10: H2B

MacromoleculeName: H2B / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MPEPSKSAPA PKKGSKKAIT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-B

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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 / Instrument: FEI VITROBOT MARK IV

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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: 3.4 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: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21698
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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