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- PDB-9z06: Structure of human lymphoid-specific helicase HELLS in its auto-i... -

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Basic information

Entry
Database: PDB / ID: 9z06
TitleStructure of human lymphoid-specific helicase HELLS in its auto-inhibitory state
ComponentsLymphoid-specific helicase
KeywordsDNA BINDING PROTEIN / lymphoid-specific helicase / SF2 chromatin remodeler / ICF syndrome / ATP-binding / Chromatin-binding
Function / homology
Function and homology information


urogenital system development / lymphocyte proliferation / chromosomal DNA methylation maintenance following DNA replication / pericentric heterochromatin formation / TGFBR3 expression / chromatin-protein adaptor activity / ATP-dependent chromatin remodeler activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of intrinsic apoptotic signaling pathway ...urogenital system development / lymphocyte proliferation / chromosomal DNA methylation maintenance following DNA replication / pericentric heterochromatin formation / TGFBR3 expression / chromatin-protein adaptor activity / ATP-dependent chromatin remodeler activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of intrinsic apoptotic signaling pathway / chromosome, centromeric region / pericentric heterochromatin / cellular response to leukemia inhibitory factor / helicase activity / kidney development / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair / site of double-strand break / cell division / hydrolase activity / apoptotic process / chromatin binding / ATP binding / nucleus
Similarity search - Function
HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / 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 ...HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / 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
Lymphoid-specific helicase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsKaur, G. / Horton, J.R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure of human lymphoid-specific helicase HELLS in its autoinhibited state.
Authors: Gundeep Kaur / Ren Ren / Jisun Lee / John R Horton / Xing Zhang / Yang Gao / Taiping Chen / Xiaodong Cheng /
Abstract: Helicase, Lymphoid Specific (HELLS), also known as Lymphoid-Specific Helicase (LSH), is a member of the SNF2 chromatin-remodeling family that regulates DNA methylation and heterochromatin ...Helicase, Lymphoid Specific (HELLS), also known as Lymphoid-Specific Helicase (LSH), is a member of the SNF2 chromatin-remodeling family that regulates DNA methylation and heterochromatin organization. Unlike most chromatin remodelers, HELLS is catalytically inactive in its apo form and requires the DNA-binding protein CDCA7 for activation, though the underlying mechanism has remained unclear. Here, we combine biochemical, biophysical, and cryo-electron microscopy analyses to define the structural basis of HELLS autoinhibition. HELLS alone assembles into a hexameric (trimer of dimers) architecture stabilized by interactions between its N-terminal coiled-coil (CC) domain and ATPase Lobe-1, while ATPase Lobe-2 remains flexible and disengaged. The CC domain functions both as an oligomerization scaffold and as an autoinhibitory module that restricts catalytic activity. Binding of CDCA7 and DNA promotes formation of an active HELLS-CDCA7-DNA ternary complex. CDCA7 recognizes hemimethylated CpG dinucleotides in both B-form and non-B-form DNA and stimulates HELLS ATPase activity. Together, these findings reveal the mechanism of HELLS autoinhibition and its activation by CDCA7 and DNA, providing new insight into how the HELLS-CDCA7-DNA ternary complex maintains DNA methylation and heterochromatin integrity.
History
DepositionOct 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 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

Downloads & links

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Assembly

Deposited unit
A: Lymphoid-specific helicase
B: Lymphoid-specific helicase
C: Lymphoid-specific helicase
D: Lymphoid-specific helicase
E: Lymphoid-specific helicase
F: Lymphoid-specific helicase


Theoretical massNumber of molelcules
Total (without water)583,3086
Polymers583,3086
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homohexamer, light scattering, DLS: homohexamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Lymphoid-specific helicase / Proliferation-associated SNF2-like protein / SWI/SNF2-related matrix-associated actin-dependent ...Proliferation-associated SNF2-like protein / SWI/SNF2-related matrix-associated actin-dependent regulator of chromatin subfamily A member 6


Mass: 97217.992 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HELLS, PASG, SMARCA6, Nbla10143 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NRZ9, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
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: Human HELLS / Type: COMPLEX / Details: Uniprot# Q9NRZ9 / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.56 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCL1
2150 mMSodium chlorideNaCl1
35 %Glycerol1
40.5 mMTCEP1
51 mMMagnesium chlorideMgCl21
60.02 mMATPgammaS1
71
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse, homogenous
Specimen supportDetails: 20 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 273.1 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 58.51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12544

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2Leginonimage acquisition
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraX1.9model fitting
10cryoSPARC4.5.3final Euler assignment
11cryoSPARC4.5.3classification
12cryoSPARC4.5.33D reconstruction
13PHENIX1.21.2_5419model refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65847 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 88.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00715851
ELECTRON MICROSCOPYf_angle_d1.084721379
ELECTRON MICROSCOPYf_chiral_restr0.06612359
ELECTRON MICROSCOPYf_plane_restr0.00892711
ELECTRON MICROSCOPYf_dihedral_angle_d16.44226071

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