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- PDB-21vv: Cryo-EM structure of ncBAF bound to the nucleosome -

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Entry
Database: PDB / ID: 21vv
TitleCryo-EM structure of ncBAF bound to the nucleosome
Components
  • (DNA (167-MER)) x 2
  • Actin, cytoplasmic 1
  • Actin-like protein 6A
  • B-cell CLL/lymphoma 7 protein family member A
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • SMARCA4 isoform 2
KeywordsNUCLEAR PROTEIN/DNA / Chromatin remodeling complex / ncBAF complex / nucleosome / SMARCA4 / BCL7 / ARP / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / neural retina development / npBAF complex / brahma complex / nBAF complex ...regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) 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) / neuron projection arborization / morphogenesis of a polarized epithelium / 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 / blastocyst formation / Regulation of CDH1 Function / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / tight junction / Sensory processing of sound by inner hair cells of the cochlea / 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 / transporter regulator activity / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / motor behavior / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / establishment or maintenance of cell polarity / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / cortical cytoskeleton / regulation of DNA replication / nitric-oxide synthase binding / regulation of embryonic development / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / kinesin binding / ATP-dependent activity, acting on DNA / regulation of DNA repair / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / axonogenesis / substantia nigra development / telomere maintenance / calyx of Held / nitric-oxide synthase regulator activity / positive regulation of DNA repair / helicase activity / FCGR3A-mediated phagocytosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / adherens junction / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / negative regulation of cell growth / Regulation of actin dynamics for phagocytic cup formation / B-WICH complex positively regulates rRNA expression
Similarity search - Function
BCL7 / BCL7, N-terminal conserver region / SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. ...BCL7 / BCL7, N-terminal conserver region / SWI/SNF complex subunit BRG1 / 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 / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related 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 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. / ATPase, nucleotide binding domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / Actin-like protein 6A / Actin, cytoplasmic 1 / Histone H4 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / Actin-like protein 6A / Actin, cytoplasmic 1 / Histone H4 / B-cell CLL/lymphoma 7 protein family member A / Histone H2A / SMARCA4 isoform 2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsXu, W. / Cheng, J. / Chen, Y.
Funding support China, 1items
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 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
N: B-cell CLL/lymphoma 7 protein family member A
X: DNA (167-MER)
Y: DNA (167-MER)
I: SMARCA4 isoform 2
J: Actin, cytoplasmic 1
K: Actin-like protein 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,90117
Polymers518,38414
Non-polymers5183
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 8 types, 12 molecules AEBFCGDHNIJK

#1: Protein Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0U496
#5: Protein B-cell CLL/lymphoma 7 protein family member A


Mass: 23671.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BCL7A full length with a C-terminal 6xHis tag / Source: (gene. exp.) Homo sapiens (human) / Gene: BCL7A / Production host: Homo sapiens (human) / References: UniProt: Q4VC05
#8: Protein SMARCA4 isoform 2 / SWI/SNF related / matrix associated / actin dependent regulator of chromatin / subfamily a / member 4


Mass: 191867.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SMARCA4 full length with an N-terminal 10aa linker and a C-terminal 3xFlag tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, hCG_29955 / Production host: Homo sapiens (human) / References: UniProt: Q9HBD4
#9: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 42611.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACTB full length with a C-terminal 6xHis tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Homo sapiens (human)
References: UniProt: P60709, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#10: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 48338.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACTL6A full length with a C-terminal 6xHis tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ACTL6A, BAF53, BAF53A, INO80K / Production host: Homo sapiens (human) / References: UniProt: O96019

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DNA chain , 2 types, 2 molecules XY

#6: DNA chain DNA (167-MER)


Mass: 51333.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#7: DNA chain DNA (167-MER)


Mass: 51773.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 3 molecules

#11: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1The ncBAF-NCP complexCOMPLEXThe ncBAF complex bound to a nucleosome#1-#100RECOMBINANT
2The ncBAF complexCOMPLEXOnly BCL7A, SMARCA4,ACTB, and ACT6A are observed in density map.#5, #8-#101RECOMBINANT
3NucleosomeCOMPLEXThe nucleosome core particle composed of Histones H2A, H2B, H3, H4, and double-stranded DNA. BCL7 finger helix is also included.#1-#71RECOMBINANT
4The ATPase domain of SMARCA4COMPLEXIt includes ATPase domain of SMARCA4#82RECOMBINANT
5The ARP moduleCOMPLEXThe ARP module is composed of ACTB, ACTL6A, ABM of BCL7A,and HSA of SMARCA4#5, #8-#102RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.9 MDaNO
220.7 MDaNO
330.2 MDaNO
440.19 MDaNO
550.11 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
55Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
55Homo sapiens (human)9606
Buffer solutionpH: 8
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.
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMPotasium ChlorideKCl1
220 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
32 mMMagnesium ChlorideMgCl21
42 mMDithiothreitolDTT1
50.5 mMAdenosine diphosphateADP1
68 mMSodium FlorideNaF1
71 mMBeryllium sulfateBeSO41
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF ChimeraXmodel fitting
12cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 14128693
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22221 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Details: We docked the AlphaFold3-predicted ARP module and refined ATPase-NCP model by rigid body fit, due to the limited resolution.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17Y8R

7y8r

17Y8R1PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 4.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324277
ELECTRON MICROSCOPYf_angle_d0.54533950
ELECTRON MICROSCOPYf_dihedral_angle_d23.1339574
ELECTRON MICROSCOPYf_chiral_restr0.0373811
ELECTRON MICROSCOPYf_plane_restr0.0043361

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