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- EMDB-68033: CryoEM map of the ATPase domain of SMARCA4 and the finger helix o... -

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Basic information

Entry
Database: EMDB / ID: EMD-68033
TitleCryoEM map of the ATPase domain of SMARCA4 and the finger helix of BCL7A bound to a nucleosome
Map data
Sample
  • Complex: ncBAF ATPase and BCL7A interacted with NCP complex
    • Complex: Nucleosome
      • Protein or peptide: x 4 types
      • DNA: x 2 types
    • Complex: ncBAF complex
      • Complex: ATPase module
        • Protein or peptide: x 1 types
      • Complex: ARP module
        • Protein or peptide: x 3 types
      • Protein or peptide: x 5 types
KeywordsNUCLEAR PROTEIN/DNA / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


prostate gland development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / neural retina development / npBAF complex / brahma complex ...prostate gland development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / neural retina development / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / morphogenesis of a polarized epithelium / neuron projection arborization / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Gap junction degradation / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / protein localization to adherens junction / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / dense body / Folding of actin by CCT/TriC / Tat protein binding / postsynaptic actin cytoskeleton / Ino80 complex / RSC-type complex / XY body / blastocyst formation / Regulation of CDH1 Function / regulation of double-strand break repair / Prefoldin mediated transfer of substrate to CCT/TriC / regulation of nucleotide-excision repair / Adherens junctions interactions / adherens junction assembly / nucleosome disassembly / RHOF GTPase cycle / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / tight junction / Sensory processing of sound by inner hair cells of the cochlea / Interaction between L1 and Ankyrins / positive regulation of T cell differentiation / apical junction complex / positive regulation of double-strand break repair / spinal cord development / regulation of chromosome organization / maintenance of blood-brain barrier / regulation of norepinephrine uptake / positive regulation of stem cell population maintenance / transporter regulator activity / NuA4 histone acetyltransferase complex / motor behavior / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / cortical cytoskeleton / establishment or maintenance of cell polarity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / nitric-oxide synthase binding / brush border / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / regulation of synaptic vesicle endocytosis / histone reader activity / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / kinesin binding / ATP-dependent activity, acting on DNA / regulation of DNA repair / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / axonogenesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / substantia nigra development / telomere maintenance / calyx of Held / nitric-oxide synthase regulator activity / animal organ morphogenesis / positive regulation of DNA repair / male germ cell nucleus / helicase activity / FCGR3A-mediated phagocytosis / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / adherens junction / positive regulation of cell differentiation / cell motility
Similarity search - Function
GLTSCR protein, conserved region / : / Conserved region of unknown function on GLTSCR protein / BCL7 / BCL7, N-terminal conserver region / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal ...GLTSCR protein, conserved region / : / Conserved region of unknown function on GLTSCR protein / BCL7 / BCL7, N-terminal conserver region / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / SWI/SNF complex subunit BRG1 / SMARCC, C-terminal / SWIRM-associated region 1 / Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / Helicase/SANT-associated domain / HSA domain profile. / SANT domain profile. / SANT domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain superfamily / 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 H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / Histone H3 signature 1. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain, conserved site / Bromodomain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / 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 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B / Actin-like protein 6A / Actin, cytoplasmic 1 / Histone H4 / Isoform 2 of Protein SSXT / B-cell CLL/lymphoma 7 protein family member A / BRD4-interacting chromatin-remodeling complex-associated protein-like / Histone H2A / SWI/SNF complex subunit SMARCC1 ...Histone H3 / Histone H2B / Actin-like protein 6A / Actin, cytoplasmic 1 / Histone H4 / Isoform 2 of Protein SSXT / B-cell CLL/lymphoma 7 protein family member A / BRD4-interacting chromatin-remodeling complex-associated protein-like / Histone H2A / SWI/SNF complex subunit SMARCC1 / Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / Bromodomain-containing protein 9 / SMARCA4 isoform 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsXu W / Chen Y / Cheng J
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA1800403 China
CitationJournal: Journal of Molecular Cell Biology / Year: 2026
Title: Structural basis of complex assembly and nucleosome recognition by the chromatin remodeling ncBAF complex
Authors: Xu W / Ma S / Li Y / Li M / Li C / Yin Y / Li Q / Cheng J / Chen Y
History
DepositionDec 29, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68033.png

Downloads & links

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Map

FileDownload / File: emd_68033.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00213
Minimum - Maximum-0.121756405 - 0.17551707
Average (Standard dev.)-0.000008461232 (±0.002336325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68033_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68033_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : ncBAF ATPase and BCL7A interacted with NCP complex

EntireName: ncBAF ATPase and BCL7A interacted with NCP complex
Components
  • Complex: ncBAF ATPase and BCL7A interacted with NCP complex
    • Complex: Nucleosome
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • DNA: 0N20 DNA Top Strand
      • DNA: 0N20 DNA Bottom Strand
    • Complex: ncBAF complex
      • Complex: ATPase module
        • Protein or peptide: SMARCA4
      • Complex: ARP module
        • Protein or peptide: ACTB
        • Protein or peptide: ACTL6A
        • Protein or peptide: BCL7A
      • Protein or peptide: SMARCC1
      • Protein or peptide: GLTSCR1L
      • Protein or peptide: BRD9
      • Protein or peptide: SMARCD1
      • Protein or peptide: SS18

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Supramolecule #1: ncBAF ATPase and BCL7A interacted with NCP complex

SupramoleculeName: ncBAF ATPase and BCL7A interacted with NCP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 900 KDa

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Supramolecule #2: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #10-#15
Molecular weightTheoretical: 200 KDa

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Supramolecule #3: ncBAF complex

SupramoleculeName: ncBAF complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#9
Molecular weightTheoretical: 700 KDa

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Supramolecule #4: ATPase module

SupramoleculeName: ATPase module / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #1
Molecular weightTheoretical: 190 KDa

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Supramolecule #5: ARP module

SupramoleculeName: ARP module / type: complex / ID: 5 / Parent: 3 / Macromolecule list: #2-#4
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: SMARCA4

MacromoleculeName: SMARCA4 / type: protein_or_peptide / ID: 1
Details: This construct contains a extra N-terminal linker GPGGSGGSGT and a C-terminal 3x Flag tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GPGGSGGSGT MSTPDPPLG GTPRPGPSPG PGPSPGAMLG PSPGPSPGSA HSMMGPSPGP PSAGHPIPTQ G PGGYPQDN MHQMHKPMES MHEKGMSDDP RYNQMKGMGM RSGGHAGMGP PPSPMDQHSQ GY PSPLGGS EHASSPVPAS GPSSGPQMSS GPGGAPLDGA ...String:
GPGGSGGSGT MSTPDPPLG GTPRPGPSPG PGPSPGAMLG PSPGPSPGSA HSMMGPSPGP PSAGHPIPTQ G PGGYPQDN MHQMHKPMES MHEKGMSDDP RYNQMKGMGM RSGGHAGMGP PPSPMDQHSQ GY PSPLGGS EHASSPVPAS GPSSGPQMSS GPGGAPLDGA DPQALGQQNR GPTPFNQNQL HQL RAQIMA YKMLARGQPL PDHLQMAVQG KRPMPGMQQQ MPTLPPPSVS ATGPGPGPGP GPGP GPGPA PPNYSRPHGM GGPNMPPPGP SGVPPGMPGQ PPGGPPKPWP EGPMANAAAP TSTPQ KLIP PQPTGRPSPA PPAVPPAASP VMPPQTQSPG QPAQPAPMVP LHQKQSRITP IQKPRG LDP VEILQEREYR LQARIAHRIQ ELENLPGSLA GDLRTKATIE LKALRLLNFQ RQLRQEV VV CMRRDTALET ALNAKAYKRS KRQSLREARI TEKLEKQQKI EQERKRRQKH QEYLNSIL Q HAKDFKEYHR SVTGKIQKLT KAVATYHANT EREQKKENER IEKERMRRLM AEDEEGYRK LIDQKKDKRL AYLLQQTDEY VANLTELVRQ HKAAQVAKEK KKKKKKKKAE NAEGQTPAIG PDGEPLDET SQMSDLPVKV IHVESGKILT GTDAPKAGQL EAWLEMNPGY EVAPRSDSEE S GSEEEEEE EEEEQPQAAQ PPTLPVEEKK KIPDPDSDDV SEVDARHIIE NAKQDVDDEY GV SQALARG LQSYYAVAHA VTERVDKQSA LMVNGVLKQY QIKGLEWLVS LYNNNLNGIL ADE MGLGKT IQTIALITYL MEHKRINGPF LIIVPLSTLS NWAYEFDKWA PSVVKVSYKG SPAA RRAFV PQLRSGKFNV LLTTYEYIIK DKHILAKIRW KYMIVDEGHR MKNHHCKLTQ VLNTH YVAP RRLLLTGTPL QNKLPELWAL LNFLLPTIFK SCSTFEQWFN APFAMTGEKV DLNEEE TIL IIRRLHKVLR PFLLRRLKKE VEAQLPEKVE YVIKCDMSAL QRVLYRHMQA KGVLLTD GS EKDKKGKGGT KTLMNTIMQL RKICNHPYMF QHIEESFSEH LGFTGGIVQG LDLYRASG K FELLDRILPK LRATNHKVLL FCQMTSLMTI MEDYFAYRGF KYLRLDGTTK AEDRGMLLK TFNEPGSEYF IFLLSTRAGG LGLNLQSADT VIIFDSDWNP HQDLQAQDRA HRIGQQNEVR VLRLCTVNS VEEKILAAAK YKLNVDQKVI QAGMFDQKSS SHERRAFLQA ILEHEEQDES R HCSTGSGS ASFAHTAPPP AGVNPDLEEP PLKEEDEVPD DETVNQMIAR HEEEFDLFMR MD LDRRREE ARNPKRKPRL MEEDELPSWI IKDDAEVERL TCEEEEEKMF GRGSRHRKEV DYS DSLTEK QWLKKITGKD IHDTASSVAR GLQFQRGLQF CTRASKAIEE GTLEEIEEEV RQKK SSRKR KRDSDAGSST PTTSTRSRDK DDESKKQKKR GRPPAEKLSP NPPNLTKKMK KIVDA VIKY KDSSSGRQLS EVFIQLPSRK ELPEYYELIR KPVDFKKIKE RIRNHKYRSL NDLEKD VML LCQNAQTFNL EGSLIYEDSI VLQSVFTSVR QKIEKEDDSE GEESEEEEEG EEEGSES ES RSVKVKIKLG RKEKAQDRLK GGRRRPSRGS RAKPVVSDDD SEEEQEEDRS GSGSEED DY KDHDGDYKDH DIDYKDDDDK

UniProtKB: SMARCA4 isoform 2

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Macromolecule #2: ACTB

MacromoleculeName: ACTB / type: protein_or_peptide / ID: 2
Details: This construct contains a extra C-terminal 6x His tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV THTVPIYEGY ...String:
DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV THTVPIYEGY ALPHAILRLD L AGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLS GGTTMY PGIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQ EYDES GPSIVHRKCF HHHHHH

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #3: ACTL6A

MacromoleculeName: ACTL6A / type: protein_or_peptide / ID: 3
Details: This construct contains a extra C-terminal 6x His tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: SGGVYGGDEV GALVFDIGSY TVRAGYAGED CPKVDFPTAI GMVVERDDGS TLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLKN GMVEDWDSFQ AILDHTYKMH VKSEASLHPV LMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA FANGRSTGLI ...String:
SGGVYGGDEV GALVFDIGSY TVRAGYAGED CPKVDFPTAI GMVVERDDGS TLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLKN GMVEDWDSFQ AILDHTYKMH VKSEASLHPV LMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA FANGRSTGLI LDSGATHTTA I PVHDGYVL QQGIVKSPLA GDFITMQCRE LFQEMNIELV PPYMIASKEA VREGSPANWK RK EKLPQVT RSWHNYMCNC VIQDFQASVL QVSDSTYDEQ VAAQMPTVHY EFPNGYNCDF GAE RLKIPE GLFDPSNVKG LSGNTMLGVS HVVTTSVGMC DIDIRPGLYG SVIVAGGNTL IQSF TDRLN RELSQKTPPS MRLKLIANNT TVERRFSSWI GGSILASLGT FQQMWISKQE YEEGG KQCV ERKCP HHHH HH

UniProtKB: Actin-like protein 6A

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Macromolecule #4: BCL7A

MacromoleculeName: BCL7A / type: protein_or_peptide / ID: 4
Details: This construct contains a extra C-terminal 6x His tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: SGRSVRAETR SRAKDDIKRV MAAIEKVRKW EKKWVTVGDT SLRIYKWVPV TEPKVDDKN KNKKKGKDEK CGSEVTTPEN SSSPGMMDMH DDNSNQSSIA DASPIKQENS SNSSPAPEPN SAVPSDGTE AKVDEAQADG KEHPGAEDAS DEQNSQSSME HSMNSSEKVD ...String:
SGRSVRAETR SRAKDDIKRV MAAIEKVRKW EKKWVTVGDT SLRIYKWVPV TEPKVDDKN KNKKKGKDEK CGSEVTTPEN SSSPGMMDMH DDNSNQSSIA DASPIKQENS SNSSPAPEPN SAVPSDGTE AKVDEAQADG KEHPGAEDAS DEQNSQSSME HSMNSSEKVD RQPSGDSGLA A ETSAISQD LEGVPPSKKM KLEASQQNSE EM HHHHHH

UniProtKB: B-cell CLL/lymphoma 7 protein family member A

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Macromolecule #5: SMARCC1

MacromoleculeName: SMARCC1 / type: protein_or_peptide / ID: 5
Details: This construct contains a extra C-terminal 6x His tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: AAAAGGGGPG TAVGATGSGI AAAAAGLAVY RRKDGGPATK FWESPETVSQ LDSVRVWLG KHYKKYVHAD APTNKTLAGL VVQLLQFQED AFGKHVTNPA FTKLPAKCFM DFKAGGALCH ILGAAYKYK NEQGWRRFDL QNPSRMDRNV EMFMNIEKTL VQNNCLTRPN ...String:
AAAAGGGGPG TAVGATGSGI AAAAAGLAVY RRKDGGPATK FWESPETVSQ LDSVRVWLG KHYKKYVHAD APTNKTLAGL VVQLLQFQED AFGKHVTNPA FTKLPAKCFM DFKAGGALCH ILGAAYKYK NEQGWRRFDL QNPSRMDRNV EMFMNIEKTL VQNNCLTRPN IYLIPDIDLK L ANKLKDII KRHQGTFTDE KSKASHHIYP YSSSQDDEEW LRPVMRKEKQ VLVHWGFYPD SY DTWVHSN DVDAEIEDPP IPEKPWKVHV KWILDTDIFN EWMNEEDYEV DENRKPVSFR QRI STKNEE PVRSPERRDR KASANARKRK HSPSPPPPTP TESRKKSGKK GQASLYGKRR SQKE EDEQE DLTKDMEDPT PVPNIEEVVL PKNVNLKKDS ENTPVKGGTV ADLDEQDEET VTAGG KEDE DPAKGDQSRS VDLGEDNVTE QTNHIIIPSY ASWFDYNCIH VIERRALPEF FNGKNK SKT PEIYLAYRNF MIDTYRLNPQ EYLTSTACRR NLTGDVCAVM RVHAFLEQWG LVNYQVD PE SRPMAMGPPP TPHFNVLADT PSGLVPLHLR SPQVPAAQQM LNFPEKNKEK PVDLQNFG L RTDIYSKKTL AKSKGASAGR EWTEQETLLL LEALEMYKDD WNKVSEHVGS RTQDECILH FLRLPIEDPY LENSDASLGP LAYQPVPFSQ SGNPVMSTVA FLASVVDPRV ASAAAKAALE EFSRVREEV PLELVEAHVK KVQEAARASG KVDPTYGLES SCIAGTGPDE PEKLEGAEEE K MEADPDGQ QPEKAENKVE NETDEGDKAQ DGENEKNSEK EQDSEVSEDT KSEEKETEEN KE LTDTCKE RESDTGKKKV EHEISEGNVA TAAAAALASA ATKAKHLAAV EERKIKSLVA LLV ETQMKK LEIKLRHFEE LETIMDREKE ALEQQRQQLL TERQNFHMEQ LKYAELRARQ QMEQ QQHGQ NPQQAHQHSG GPGLAPLGAA GHPGMMPHQQ PPPYPLMHHQ MPPPHPPQPG QIPGP GSMM PGQHMPGRMI PTVAANIHPS GSGPTPPGMP PMPGNILGPR VPLTAPNGMY PPPPQQ QPP PPPPADGVPP PPAPGPPASA AP HHHHHH

UniProtKB: SWI/SNF complex subunit SMARCC1

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Macromolecule #6: GLTSCR1L

MacromoleculeName: GLTSCR1L / type: protein_or_peptide / ID: 6
Details: This construct is a truncation of 1-962 amino acids and contains a extra N-terminal linker GPGGSGGSGT and a C-terminal 6x His tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GPGGSGGSGT MDDDDDSCL LDLIGDPQAL NYFLHGPSNK SSNDDLTNAG YSAANSNSIF ANSSNADPKS SLKGVSNQLG EGPSDGLPLS SSLQFLEDEL ESSPLPDLTE DQPFDILQKS LQEANITEQT LAEEAYLDAS IGSSQQFAQA QLHPSSSASF TQASNVSNYS ...String:
GPGGSGGSGT MDDDDDSCL LDLIGDPQAL NYFLHGPSNK SSNDDLTNAG YSAANSNSIF ANSSNADPKS SLKGVSNQLG EGPSDGLPLS SSLQFLEDEL ESSPLPDLTE DQPFDILQKS LQEANITEQT LAEEAYLDAS IGSSQQFAQA QLHPSSSASF TQASNVSNYS GQTLQPIGVT HVPVGASFAS NTVGVQHGFM QHVGISVPSQ HLSNSSQISG SGQIQLIGSF GNHPSMMTIN NLDGSQIILK GSGQQAPSNV SGGLLVHRQT PNGNSLFGNS SSSPVAQPVT VPFNSTNFQT SLPVHNIIIQ RGLAPNSNKV PINIQPKPIQ MGQQNTYNVN NLGIQQHHVQ QGISFASASS PQGSVVGPHM SVNIVNQQNT RKPVTSQAVS STGGSIVIHS PMGQPHAPQS QFLIPTSLSV SSNSVHHVQT INGQLLQTQP SQLISGQVAS EHVMLNRNSS NMLRTNQPYT GPMLNNQNTA VHLVSGQTFA ASGSPVIANH ASPQLVGGQM PLQQASPTVL HLSPGQSSVS QGRPGFATMP SVTSMSGPSR FPAVSSASTA HPSLGSAVQS GSSGSNFTGD QLTQPNRTPV PVSVSHRLPV SSSKSTSTFS NTPGTGTQQQ FFCQAQKKCL NQTSPISAPK TTDGLRQAQI PGLLSTTLPG QDSGSKVISA SLGTAQPQQE KVVGSSPGHP AVQVESHSGG QKRPAAKQLT KGAFILQQLQ RDQAHTVTPD KSHFRSLSDA VQRLLSYHVC QGSMPTEEDL RKVDNEFETV ATQLLKRTQA MLNKYRCLLL EDAMRINPSA EMVMIDRMFN QEERASLSRD KRLALVDPEG FQADFCCSFK LDKAAHETQF GRSDQHGSKA SSSLQPPAKA QGRDRAKTGV TEPMNHDQFH LVPNHIVVSA EGNISKKTEC LGRALKFDKV GLVQYQSTSE EKASRREPLK ASQCSPGPEG HRKTSSRSDH GTESKLSSIL ADS HHHHHH

UniProtKB: BRD4-interacting chromatin-remodeling complex-associated protein-like

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Macromolecule #7: BRD9

MacromoleculeName: BRD9 / type: protein_or_peptide / ID: 7
Details: This construct contains a extra N-terminal linker GPGGSGGSGT.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GPGGSGGSGT MGKKHKKHK AEWRSSYEDY ADKPLEKPLK LVLKVGGSEV TELSGSGHDS SYYDDRSDHE R ERHKEKKK KKKKKSEKEK HLDDEERRKR KEEKKRKRER EHCDTEGEAD DFDPGKKVEV EP PPDRPVR ACRTQPAENE STPIQQLLEH FLRQLQRKDP ...String:
GPGGSGGSGT MGKKHKKHK AEWRSSYEDY ADKPLEKPLK LVLKVGGSEV TELSGSGHDS SYYDDRSDHE R ERHKEKKK KKKKKSEKEK HLDDEERRKR KEEKKRKRER EHCDTEGEAD DFDPGKKVEV EP PPDRPVR ACRTQPAENE STPIQQLLEH FLRQLQRKDP HGFFAFPVTD AIAPGYSMII KHP MDFGTM KDKIVANEYK SVTEFKADFK LMCDNAMTYN RPDTVYYKLA KKILHAGFKM MSKQ AALLG NEDTAVEEPV PEVVPVQVET AKKSKKPSRE VISCMFEPEG NACSLTDSTA EEHVL ALVE HAADEARDRI NRFLPGGKMG YLKRNGDGSL LYSVVNTAEP DADEEETHPV DLSSLS SKL LPGFTTLGFK DERRNKVTFL SSATTALSMQ NNSVFGDLKS DEMELLYSAY GDETGVQ CA LSLQEFVKDA GSYSKKVVDD LLDQITGGDH SRTLFQLKQR RNVPMKPPDE AKVGDTLG D SSSSVLEFMS MKSYPDVSVD ISMLSSLGKV KKELDPDDSH LNLDETTKLL QDLHEAQAE RGGSRPSSNL SSLSNASERD QHHLGSPSRL SVGEQPDVTH DPYEFLQSPE PAASAKT

UniProtKB: Bromodomain-containing protein 9

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Macromolecule #8: SMARCD1

MacromoleculeName: SMARCD1 / type: protein_or_peptide / ID: 8
Details: This construct contains a extra C-terminal 3x Flag tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: AARAGFQSVA PSGGAGASGG AGAAAALGPG GTPGPPVRMG PAPGQGLYRS PMPGAAYPR PGMLPGSRMT PQGPSMGPPG YGGNPSVRPG LAQSGMDQSR KRPAPQQIQQ VQQQAVQNRN HNAKKKKMA DKILPQRIRE LVPESQAYMD LLAFERKLDQ TIMRKRLDIQ ...String:
AARAGFQSVA PSGGAGASGG AGAAAALGPG GTPGPPVRMG PAPGQGLYRS PMPGAAYPR PGMLPGSRMT PQGPSMGPPG YGGNPSVRPG LAQSGMDQSR KRPAPQQIQQ VQQQAVQNRN HNAKKKKMA DKILPQRIRE LVPESQAYMD LLAFERKLDQ TIMRKRLDIQ EALKRPIKQK R KLRIFISN TFNPAKSDAE DGEGTVASWE LRVEGRLLED SALSKYDATK QKRKFSSFFK SL VIELDKD LYGPDNHLVE WHRTATTQET DGFQVKRPGD VNVRCTVLLM LDYQPPQFKL DPR LARLLG IHTQTRPVII QALWQYIKTH KLQDPHEREF VICDKYLQQI FESQRMKFSE IPQR LHALL MPPEPIIINH VISVDPNDQK KTACYDIDVE VDDTLKTQMN SFLLSTASQQ EIATL DNKT MTDVVGNPEE ERRAEFYFQP WAQEAVCRYF YSKVQQRRQE LEQALGIRNT DYKDHDGDY KDHDIDYKDD DDK

UniProtKB: Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

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Macromolecule #9: SS18

MacromoleculeName: SS18 / type: protein_or_peptide / ID: 9
Details: This construct contains a extra C-terminal 3x Flag tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: SVAFAAPRQR GKGEITPAAI QKMLDDNNHL IQCIMDSQNK GKTSECSQYQ QMLHTNLVY LATIADSNQN MQSLLPAPPT QNMPMGPGGM NQSGPPPPPR SHNMPSDGMV GGGPPAPHMQ NQMNGQMPG PNHMPMQGPG PNQLNMTNSS MNMPSSSHGS MGGYNHSVPS ...String:
SVAFAAPRQR GKGEITPAAI QKMLDDNNHL IQCIMDSQNK GKTSECSQYQ QMLHTNLVY LATIADSNQN MQSLLPAPPT QNMPMGPGGM NQSGPPPPPR SHNMPSDGMV GGGPPAPHMQ NQMNGQMPG PNHMPMQGPG PNQLNMTNSS MNMPSSSHGS MGGYNHSVPS SQSMPVQNQM T MSQGQPMG NYGPRPNMSM QPNQGPMMHQ QPPSQQYNMP QGGGQHYQGQ QPPMGMMGQV NQ GNHMMGQ RQIPPYRPPQ QGPPQQYSGQ EDYYGDQYSH GGQGPPEGMN QQYYPDGNSQ YGQ QQDAYQ GPPPQQGYPP QQQQYPGQQG YPGQQQGYGP SQGGPGPQYP NYPQGQGQQY GGYR PTQPG PPQPPQQRPY GYDQGQYGNY QQ DYKDHDG DYKDHDIDYK DDDDK

UniProtKB: Isoform 2 of Protein SSXT

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Macromolecule #10: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGN A ARDNKKTRII PRHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #11: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFE R IAGEASRLAH YNKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B

+
Macromolecule #12: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

+
Macromolecule #13: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

+
Macromolecule #14: 0N20 DNA Top Strand

MacromoleculeName: 0N20 DNA Top Strand / type: dna / ID: 14 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
CTGGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCCTGTGCA TGTATTGAAC AGCGACC

+
Macromolecule #15: 0N20 DNA Bottom Strand

MacromoleculeName: 0N20 DNA Bottom Strand / type: dna / ID: 15 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
GGTCGCTGTT CAATACATGC ACAGGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTAA AACGCGGGGG ACAGCGCGTA CGTGCGTTTA AGCGGTGCTA GAGCTGTCTA CGACCAATTG AGCGGCCTCG GCACCGGGAT TCTCCAG

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMKClPotassium Chloride
20.0 mMHEPESN-2-Hydroxyethylpiperazine-N-2-Ethane Sulfonic Acid
2.0 mMDTTDithiothreitol
2.0 mMMgCl2Magnesium Chloride
0.5 mMADPAdenosine diphosphate
8.0 mMNaFSodium Fluoride
1.0 mMBeSO4Beryllium Sulfate

Details: 20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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 / Cs: 0.01 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
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

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 73906
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
Final angle assignmentType: OTHER / Software - Name: RELION / Details: relion
FSC plot (resolution estimation)

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