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- EMDB-73696: Structure of human lymphoid-specific helicase HELLS in its auto-i... -

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Basic information

Entry
Database: EMDB / ID: EMD-73696
TitleStructure of human lymphoid-specific helicase HELLS in its auto-inhibitory state
Map datacryoSPARC sharpened map
Sample
  • Complex: Human HELLS
    • Protein or peptide: Human lymphoid-specific helicase HELLS
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: 3.47 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_73696.png

Downloads & links

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Map

FileDownload / File: emd_73696.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
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AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 300 pix.
= 496.2 Å		1.65 Å/pix.
x 300 pix.
= 496.2 Å		1.65 Å/pix.
x 300 pix.
= 496.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.274
Minimum - Maximum-2.7184467 - 5.374529
Average (Standard dev.)-0.0009694291 (±0.06425187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 496.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer sharpened map

Fileemd_73696_additional_1.map
AnnotationdeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: cryoSPARC sharpened half map A

Fileemd_73696_half_map_1.map
AnnotationcryoSPARC sharpened half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoSPARC sharpened half map B

Fileemd_73696_half_map_2.map
AnnotationcryoSPARC sharpened half map B
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 HELLS

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

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Supramolecule #1: Human HELLS

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

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Macromolecule #1: Human lymphoid-specific helicase HELLS

MacromoleculeName: Human lymphoid-specific helicase HELLS / type: protein_or_peptide / ID: 1 / Details: UNIPROT Q9NRZ9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPAERPAGSG GSEAPAMVEQ LDTAVITPAM LEEEEQLEAA GLERERKMLE KARMSWDRES TEIRYRRLQH LLEKSNIYSK FLLTKMEQQQ LEEQKKKEKL ERKKESLKVK KGKNSIDASE EKPVMRKKRG REDESYNISE VMSKEEILSV AKKNKKENED ENSSSTNLCV ...String:
MPAERPAGSG GSEAPAMVEQ LDTAVITPAM LEEEEQLEAA GLERERKMLE KARMSWDRES TEIRYRRLQH LLEKSNIYSK FLLTKMEQQQ LEEQKKKEKL ERKKESLKVK KGKNSIDASE EKPVMRKKRG REDESYNISE VMSKEEILSV AKKNKKENED ENSSSTNLCV EDLQKNKDSN SIIKDRLSET VRQNTKFFFD PVRKCNGQPV PFQQPKHFTG GVMRWYQVEG MEWLRMLWEN GINGILADEM GLGKTVQCIA TIALMIQRGV PGPFLVCGPL STLPNWMAEF KRFTPDIPTM LYHGTQEERQ KLVRNIYKRK GTLQIHPVVI TSFEIAMRDR NALQHCYWKY LIVDEGHRIK NMKCRLIREL KRFNADNKLL LTGTPLQNNL SELWSLLNFL LPDVFDDLKS FESWFDITSL SETAEDIIAK EREQNVLHML HQILTPFLLR RLKSDVALEV PPKREVVVYA PLSKKQEIFY TAIVNRTIAN MFGSSEKETI ELSPTGRPKR RTRKSINYSK IDDFPNELEK LISQIQPEVD RERAVVEVNI PVESEVNLKL QNIMMLLRKC CNHPYLIEYP IDPVTQEFKI DEELVTNSGK FLILDRMLPE LKKRGHKVLL FSQMTSMLDI LMDYCHLRDF NFSRLDGSMS YSEREKNMHS FNTDPEVFIF LVSTRAGGLG INLTAADTVI IYDSDWNPQS DLQAQDRCHR IGQTKPVVVY RLVTANTIDQ KIVERAAAKR KLEKLIIHKN HFKGGQSGLN LSKNFLDPKE LMELLKSRDY EREIKGSREK VISDKDLELL 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
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: 3.47 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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