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- PDB-21wa: Cryo-EM structure of the ATPase domain of SMARCA4 bound to a nucl... -

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Basic information

Entry
Database: PDB / ID: 21wa
TitleCryo-EM structure of the ATPase domain of SMARCA4 bound to a nucleosome
Components
  • (DNA (167-MER)) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • SMARCA4 isoform 2
KeywordsNUCLEAR PROTEIN/DNA / Chromatin remodeling complex / nucleosome / SMARCA4 / ATPase / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


SWI/SNF complex / ATP-dependent activity, acting on DNA / helicase activity / negative regulation of cell growth / fibrillar center / structural constituent of chromatin / nucleosome / nervous system development / heterochromatin formation / nucleosome assembly ...SWI/SNF complex / ATP-dependent activity, acting on DNA / helicase activity / negative regulation of cell growth / fibrillar center / structural constituent of chromatin / nucleosome / nervous system development / heterochromatin formation / nucleosome assembly / histone binding / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / hydrolase activity / nucleolus / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
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 ...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 / : / 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. / 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 / Histone H4 / 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: 3.7 Å
AuthorsXu, W. / Chen, Y. / Cheng, J.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
I: SMARCA4 isoform 2
X: DNA (167-MER)
Y: DNA (167-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,27914
Polymers403,76211
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 , 5 types, 9 molecules AEBFCGDHI

#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 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

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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: Escherichia coli (E. coli)
#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: Escherichia coli (E. coli)

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Non-polymers , 3 types, 3 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

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Details

Has ligand of interestN
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

ComponentName: The ATPase domain of SMARCA4 bound to a nucleosome / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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
4CTFFIND4CTF correction
12RELION3D reconstruction
13PHENIX1.20.1_4487model refinement
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.7FSC 0.143 CUT-OFF148530121WAPOINT
23.7FSC 0.143 CUT-OFF148530121WAPOINT
33.7FSC 0.143 CUT-OFF148530121WAPOINT
43.7FSC 0.143 CUT-OFF148530121WAPOINT
53.7FSC 0.143 CUT-OFF148530221WAPOINT
63.7FSC 0.143 CUT-OFF148530221WAPOINT
73.7FSC 0.143 CUT-OFF148530221WAPOINT
83.7FSC 0.143 CUT-OFF148530221WAPOINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7Y8R

7y8r


Accession code: 7Y8R / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317559
ELECTRON MICROSCOPYf_angle_d0.52624866
ELECTRON MICROSCOPYf_dihedral_angle_d25.5637075
ELECTRON MICROSCOPYf_chiral_restr0.0352809
ELECTRON MICROSCOPYf_plane_restr0.0042196

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