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- EMDB-64577: local ATPase-NCP density map of the ncBAF-nucleosome complex in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-64577
Titlelocal ATPase-NCP density map of the ncBAF-nucleosome complex in the ADP-BeFx-bound state
Map data
Sample
  • Complex: ncBAF-nucleosome complex
    • Complex: Xenopus nucleosome
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: The ARP module of ncBAF complex
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
      • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsChromatin remodeling / SWI/SNF / Epigenetics / GENE REGULATION/DNA / GENE REGULATION-DNA complex
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / nBAF complex / npBAF complex / negative regulation of androgen receptor signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex ...positive regulation of glucose mediated signaling pathway / nBAF complex / npBAF complex / negative regulation of androgen receptor signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / nucleosome array spacer activity / regulation of G0 to G1 transition / Tat protein binding / RNA polymerase I preinitiation complex assembly / host-mediated activation of viral transcription / SWI/SNF complex / ATP-dependent chromatin remodeler activity / nucleosome disassembly / regulation of mitotic metaphase/anaphase transition / nuclear androgen receptor binding / positive regulation of T cell differentiation / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / positive regulation of Wnt signaling pathway / positive regulation of signal transduction by p53 class mediator / regulation of G1/S transition of mitotic cell cycle / Chromatin modifying enzymes / DNA polymerase binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / helicase activity / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / negative regulation of cell growth / positive regulation of miRNA transcription / fibrillar center / Negative Regulation of CDH1 Gene Transcription / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosomal DNA binding / kinetochore / nuclear matrix / RMTs methylate histone arginines / innate immune response in mucosa / p53 binding / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / positive regulation of cold-induced thermogenesis / nervous system development / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / histone binding / antibacterial humoral response / chromatin organization / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / : / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex ...SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, 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 / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / 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 / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Bromodomain, conserved site / Bromodomain signature. / Histone H3 / Histone H3/CENP-A / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus (frog) / Xenopus laevis (African clawed frog) / artificial sequences (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsSun F / Zou B / Li H / Xu C / Luo Q / Wang C / Xu P / Pei D / Chen J / Qin D ...Sun F / Zou B / Li H / Xu C / Luo Q / Wang C / Xu P / Pei D / Chen J / Qin D / Zhang Y / He J
Funding support China, 6 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32361163669 China
Other government2023M743512 China
National Natural Science Foundation of China (NSFC)32170189 China
National Natural Science Foundation of China (NSFC)32241021 China
Other governmentGZC20232691 China
Other government2023A1515110923 China
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structural basis for BCL7B-mediated ncBAF-nucleosome engagement.
Authors: Fahui Sun / Binqian Zou / He Li / Chongshen Xu / Qiaohong Luo / Chi Wang / Pengqi Xu / Duanqing Pei / Jiekai Chen / Dajiang Qin / Ying Zhang / Jun He /
Abstract: The mammalian SWI/SNF family of chromatin remodelers comprises BRG1/BRM-associated factor (cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF) complexes, which slide and disassemble ...The mammalian SWI/SNF family of chromatin remodelers comprises BRG1/BRM-associated factor (cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF) complexes, which slide and disassemble nucleosomes to regulate gene expression and chromatin structure dependent on ATP hydrolysis energy. While the chromatin engagement mechanisms of cBAF and PBAF have been structurally resolved, the molecular architecture governing ncBAF interaction with chromatin remains elusive. In this study, by integrating cryo-electron microscopy, biochemical assays, and cross-linking mass spectrometry, we resolved the conformational transition of ncBAF-nucleosome complexes from nucleotide-free to nucleotide-bound states. Our analyses establish BCL7 proteins as dynamic molecular tethers connecting the ARP module to the nucleosomal acidic patch and demonstrate that BCL7B promotes ncBAF-mediated nucleosome remodeling, with BRG1-catalyzed ATP hydrolysis triggering conformational changes that modulate BCL7-mediated histone association. Structurally and biochemically, we further demonstrate that β-actin within the BCL7-containing ARP module retains ATP hydrolysis activity, rendering its exposed pointed end structurally compatible with incorporation into the barbed end of nuclear actin filaments, which provides a potential molecular basis for coordinating nuclear actin networks with chromatin remodeling. Collectively, our findings unravel a dynamic role of BCL7 in regulating ncBAF-mediated chromatin remodeling and establish a distinct chromatin engagement mode of ncBAF from that of cBAF/PBAF.
History
DepositionMay 13, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64577.png

Downloads & links

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Map

FileDownload / File: emd_64577.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.0039366186 - 2.029566
Average (Standard dev.)0.0024670616 (±0.036871787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64577_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64577_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64577_half_map_2.map
Projections & Slices
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Sample components

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Entire : ncBAF-nucleosome complex

EntireName: ncBAF-nucleosome complex
Components
  • Complex: ncBAF-nucleosome complex
    • Complex: Xenopus nucleosome
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: The ARP module of ncBAF complex
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
      • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ncBAF-nucleosome complex

SupramoleculeName: ncBAF-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Xenopus nucleosome

SupramoleculeName: Xenopus nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus (frog)

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Supramolecule #3: The ARP module of ncBAF complex

SupramoleculeName: The ARP module of ncBAF complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#7, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.163421 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NASGRGKQGG KTRAKAKTRS SRAGLQFPVG RVHRLLRKGN YAERVGAGAP VYLAAVLEYL TAEILELAGN AARDNKKTRI IPRHLQLAV RNDEELNKLL GRVTIAQGGV LPNIQSVLLP KKTESSKSAK SK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B

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Macromolecule #7: SWI/SNF-related matrix-associated actin-dependent regulator of ch...

MacromoleculeName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
type: protein_or_peptide / ID: 7 / 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: 184.934828 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MASTPDPPLG GTPRPGPSPG PGPSPGAMLG PSPGPSPGSA HSMMGPSPGP PSAGHPIPTQ GPGGYPQDNM HQMHKPMESM HEKGMSDDP RYNQMKGMGM RSGGHAGMGP PPSPMDQHSQ GYPSPLGGSE HASSPVPASG PSSGPQMSSG PGGAPLDGAD P QALGQQNR ...String:
MASTPDPPLG GTPRPGPSPG PGPSPGAMLG PSPGPSPGSA HSMMGPSPGP PSAGHPIPTQ GPGGYPQDNM HQMHKPMESM HEKGMSDDP RYNQMKGMGM RSGGHAGMGP PPSPMDQHSQ GYPSPLGGSE HASSPVPASG PSSGPQMSSG PGGAPLDGAD P QALGQQNR GPTPFNQNQL HQLRAQIMAY KMLARGQPLP DHLQMAVQGK RPMPGMQQQM PTLPPPSVSA TGPGPGPGPG PG PGPGPAP PNYSRPHGMG GPNMPPPGPS GVPPGMPGQP PGGPPKPWPE GPMANAAAPT STPQKLIPPQ PTGRPSPAPP AVP PAASPV MPPQTQSPGQ PAQPAPMVPL HQKQSRITPI QKPRGLDPVE ILQEREYRLQ ARIAHRIQEL ENLPGSLAGD LRTK ATIEL KALRLLNFQR QLRQEVVVCM RRDTALETAL NAKAYKRSKR QSLREARITE KLEKQQKIEQ ERKRRQKHQE YLNSI LQHA KDFKEYHRSV TGKIQKLTKA VATYHANTER EQKKENERIE KERMRRLMAE DEEGYRKLID QKKDKRLAYL LQQTDE YVA NLTELVPQHK AAQVAKEKKK KKKKKKAENA EGQTPAIGPD GEPLDETSQM SDLPVKVIHV ESGKILTGTD APKAGQL EA WLEMNPGYEV APRSDSEESG SEEEEEEEEE EQPQAAQPPT LPVEEKKKIP DPDSDDVSEV DARHIIENAK QDVDDEYG V SQALARGLQS YYAVAHAVTE RVDKQSALMV NGVLKQYQIK GLEWLVSLYN NNLNGILADE MGLGKTIQTI ALITYLMEH KRINGPFLII VPLSTLSNWA YEFDKWAPSV VKVSYKGSPA ARRAFVPQLR SGKFNVLLTT YEYIIKDKHI LAKIRWKYMI VDEGHRMKN HHCKLTQVLN THYVAPRRLL LTGTPLQNKL PELWALLNFL LPTIFKSCST FEQWFNAPFA MTGEKVDLNE E ETILIIRR LHKVLRPFLL RRLKKEVEAQ LPEKVEYVIK CDMSALQRVL YRHMQAKGVL LTDGSEKDKK GKGGTKTLMN TI MQLRKIC NHPYMFQHIE ESFSEHLGFT GGIVQGLDLY RASGKFELLD RILPKLRATN HKVLLFCQMT SLMTIMEDYF AYR GFKYLR LDGTTKAEDR GMLLKTFNEP GSEYFIFLLS TRAGGLGLNL QSADTVIIFD SDWNPHQDLQ AQDRAHRIGQ QNEV RVLRL CTVNSVEEKI LAAAKYKLNV DQKVIQAGMF DQKSSSHERR AFLQAILEHE EQDESRHCST GSGSASFAHT APPPA GVNP DLEEPPLKEE DEVPDDETVN QMIARHEEEF DLFMRMDLDR RREEARNPKR KPRLMEEDEL PSWIIKDDAE VERLTC EEE EEKMFGRGSR HRKEVDYSDS LTEKQWLKAI EEGTLEEIEE EVRQKKSSRK RKRDSDAGSS TPTTSTRSRD KDDESKK QK KRGRPPAEKL SPNPPNLTKK MKKIVDAVIK YKDSSSGRQL SEVFIQLPSR KELPEYYELI RKPVDFKKIK ERIRNHKY R SLNDLEKDVM LLCQNAQTFN LEGSLIYEDS IVLQSVFTSV RQKIEKEDDS EGEESEEEEE GEEEGSESES RSVKVKIKL GRKEKAQDRL KGGRRRPSRG SRAKPVVSDD DSEEEQEEDR SGSGSEED

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4

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Macromolecule #5: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: artificial sequences (others)
Molecular weightTheoretical: 51.271625 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)(DT)(DC)(DT)(DA)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC)(DC) (DA)(DC)(DC)(DG)(DC)

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Macromolecule #6: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: artificial sequences (others)
Molecular weightTheoretical: 51.840988 KDa
SequenceString: (DG)(DC)(DG)(DG)(DT)(DG)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC) ...String:
(DG)(DC)(DG)(DG)(DT)(DG)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC) (DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC) (DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC) (DT)(DC)(DC)(DA)(DG)

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Macromolecule #8: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / 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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72416
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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