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- EMDB-73693: Structure of human lymphoid-specific helicase HELLS in its auto-i... -

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Basic information

Entry
Database: EMDB / ID: EMD-73693
TitleStructure of human lymphoid-specific helicase HELLS in its auto-inhibitory state
Map datacryosparc sharpened map
Sample
  • Complex: Human lymphoid-specific helicase HELLS
    • Protein or peptide: Lymphoid-specific helicase
Keywordslymphoid-specific helicase / SF2 chromatin remodeler / ICF syndrome / ATP-binding / Chromatin-binding / DNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 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_73693.png

Downloads & links

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Map

FileDownload / File: emd_73693.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryosparc sharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 317.568 Å		0.83 Å/pix.
x 384 pix.
= 317.568 Å		0.83 Å/pix.
x 384 pix.
= 317.568 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.178
Minimum - Maximum-1.8895091 - 2.8911753
Average (Standard dev.)0.0015017088 (±0.05852342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer sharpened map

Fileemd_73693_additional_1.map
AnnotationdeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Histogram

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Half map: Cryosparc sharpened half map B

Fileemd_73693_half_map_1.map
AnnotationCryosparc sharpened half map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Cryosparc sharpened half map A

Fileemd_73693_half_map_2.map
AnnotationCryosparc sharpened half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human lymphoid-specific helicase HELLS

EntireName: Human lymphoid-specific helicase HELLS
Components
  • Complex: Human lymphoid-specific helicase HELLS
    • Protein or peptide: Lymphoid-specific helicase

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Supramolecule #1: Human lymphoid-specific helicase HELLS

SupramoleculeName: Human lymphoid-specific helicase HELLS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 560 KDa

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Macromolecule #1: Lymphoid-specific helicase

MacromoleculeName: Lymphoid-specific helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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: 97.217992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPAERPAGSG GSEAPAMVEQ LDTAVITPAM LEEEEQLEAA GLERERKMLE KARMSWDRES TEIRYRRLQH LLEKSNIYSK FLLTKMEQQ QLEEQKKKEK LERKKESLKV KKGKNSIDAS EEKPVMRKKR GREDESYNIS EVMSKEEILS VAKKNKKENE D ENSSSTNL ...String:
MPAERPAGSG GSEAPAMVEQ LDTAVITPAM LEEEEQLEAA GLERERKMLE KARMSWDRES TEIRYRRLQH LLEKSNIYSK FLLTKMEQQ QLEEQKKKEK LERKKESLKV KKGKNSIDAS EEKPVMRKKR GREDESYNIS EVMSKEEILS VAKKNKKENE D ENSSSTNL CVEDLQKNKD SNSIIKDRLS ETVRQNTKFF FDPVRKCNGQ PVPFQQPKHF TGGVMRWYQV EGMEWLRMLW EN GINGILA DEMGLGKTVQ CIATIALMIQ RGVPGPFLVC GPLSTLPNWM AEFKRFTPDI PTMLYHGTQE ERQKLVRNIY KRK GTLQIH PVVITSFEIA MRDRNALQHC YWKYLIVDEG HRIKNMKCRL IRELKRFNAD NKLLLTGTPL QNNLSELWSL LNFL LPDVF DDLKSFESWF DITSLSETAE DIIAKEREQN VLHMLHQILT PFLLRRLKSD VALEVPPKRE VVVYAPLSKK QEIFY TAIV NRTIANMFGS SEKETIELSP TGRPKRRTRK SINYSKIDDF PNELEKLISQ IQPEVDRERA VVEVNIPVES EVNLKL QNI MMLLRKCCNH PYLIEYPIDP VTQEFKIDEE LVTNSGKFLI LDRMLPELKK RGHKVLLFSQ MTSMLDILMD YCHLRDF NF SRLDGSMSYS EREKNMHSFN TDPEVFIFLV STRAGGLGIN LTAADTVIIY DSDWNPQSDL QAQDRCHRIG QTKPVVVY R LVTANTIDQK IVERAAAKRK LEKLIIHKNH FKGGQSGLNL SKNFLDPKEL MELLKSRDYE REIKGSREKV ISDKDLELL LDRSDLIDQM NASGPIKEKM GIFKILENSE DSSPECLF

UniProtKB: Lymphoid-specific helicase

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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
SoftwareName: Leginon
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 reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 338516
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
SoftwareName: UCSF ChimeraX (ver. 1.9)
Output model

PDB-9z04:
Structure of human lymphoid-specific helicase HELLS in its auto-inhibitory state

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