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- EMDB-73697: Focussed refinement map of ATPase lobe 2 of human lymphoid-specif... -

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Basic information

Entry
Database: EMDB / ID: EMD-73697
TitleFocussed refinement map of ATPase lobe 2 of human lymphoid-specific helicase HELLS
Map datacryoSPARC sharpened map
Sample
  • Complex: Human HELLS
Keywordslymphoid-specific helicase / SF2 chromatin remodeler / ICF syndrome / ATP-binding / Chromatin-binding / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.76 Å
AuthorsKaur G / Horton JR / Cheng X
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73697.png

Downloads & links

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Map

FileDownload / File: emd_73697.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoSPARC sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 300 pix.
= 495. Å		1.65 Å/pix.
x 300 pix.
= 495. Å		1.65 Å/pix.
x 300 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.789
Minimum - Maximum-19.001476 - 26.687342000000001
Average (Standard dev.)-0.0024661962 (±0.100416176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: cryosparc sharpened half map B

Fileemd_73697_half_map_1.map
Annotationcryosparc sharpened half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryosparc sharpened half map A

Fileemd_73697_half_map_2.map
Annotationcryosparc sharpened half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human HELLS

EntireName: Human HELLS
Components
  • Complex: Human HELLS

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Supramolecule #1: Human HELLS

SupramoleculeName: Human HELLS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Details: Uniprot# Q9NRZ9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 560 KDa

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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

Concentration0.25 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HCL
150.0 mMSodium chlorideNaCl
5.0 %Glycerol
0.5 mMTCEP
1.0 mMMagnesium chlorideMgCl2
0.02 mMATPgammaS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 20 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 273.1 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse, homogenous

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 12544 / Average electron dose: 58.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio from cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 204425
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model

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