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- EMDB-43612: Cryo-EM Structure of DHX36 bound to the cMyc DNA G-quadruplex, Class 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-43612
TitleCryo-EM Structure of DHX36 bound to the cMyc DNA G-quadruplex, Class 1
Map dataUnsharpened Map
Sample
  • Complex: Binary Complex of Bos taurus DHX36 bound to a DNA G-quadruplex
    • Protein or peptide: ATP-dependent DNA/RNA helicase DHX36
    • DNA: DNA (29-MER)
KeywordsDEAH-Box Helicase / Helicase / G-quadruplex / RNA / MOTOR PROTEIN
Function / homology
Function and homology information


DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / catalytic activity, acting on a nucleic acid / positive regulation of cardioblast differentiation / telomerase RNA stabilization / pre-miRNA binding / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / positive regulation of myeloid dendritic cell cytokine production ...DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / catalytic activity, acting on a nucleic acid / positive regulation of cardioblast differentiation / telomerase RNA stabilization / pre-miRNA binding / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / positive regulation of myeloid dendritic cell cytokine production / 3'-UTR-mediated mRNA destabilization / regulation of transcription by RNA polymerase III / G-quadruplex DNA binding / positive regulation of dendritic spine morphogenesis / mRNA 3'-UTR AU-rich region binding / cellular response to arsenite ion / positive regulation of cytoplasmic translation / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to exogenous dsRNA / positive regulation of interferon-alpha production / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / regulation of mRNA stability / DNA helicase activity / ossification / mRNA 3'-UTR binding / mRNA 5'-UTR binding / histone deacetylase binding / cytoplasmic stress granule / cellular response to UV / single-stranded DNA binding / double-stranded RNA binding / cellular response to heat / spermatogenesis / perikaryon / G-quadruplex RNA binding / defense response to virus / DNA helicase / cell differentiation / chromosome, telomeric region / RNA helicase activity / positive regulation of canonical NF-kappaB signal transduction / negative regulation of translation / nuclear speck / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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
ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBanco MT / Ferre-D'Amare AR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis for dual DNA and RNA specificity of the G-quadruplex-resolving DEAH-box helicase DHX36.
Authors: Michael T Banco / Tapas Paul / Jiansen Jiang / Sua Myong / Adrian R Ferré-D'Amaré /
Abstract: DEAH-box helicases, which share a structurally conserved ATPase core, function in all facets of eukaryotic gene expression. While most helicases are highly specialized for their substrates, DHX36 ...DEAH-box helicases, which share a structurally conserved ATPase core, function in all facets of eukaryotic gene expression. While most helicases are highly specialized for their substrates, DHX36 (DEAH-box helicase 36) resolves both DNA and RNA G-quadruplexes. To elucidate the molecular basis of this versatility, we have determined cryo-electron microscopy structures of bovine DHX36 bound to a three-tier RNA G-quadruplex and a six-tier DNA G-quadruplex at 2.6 and 3.4 Å resolution, respectively. Kinetic and smFRET characterizations of structure-guided mutants indicate a key role for the RecA2 domain of the helicase core in DNA vs. RNA discrimination. Furthermore, our structures show that a sequence-divergent RecA2 domain surface loop synergizes with a DHX36-specific N-terminal extension to orthogonally recognize features that specify G-quadruplexes over other nucleic acid structures. Our analysis suggests that recognizing their folded substrates by DEAH-box helicases may generally involve ornamentations of their structural cores acting synergistically with specialized peripheral elements.
History
DepositionFeb 3, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43612.png

Downloads & links

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Map

FileDownload / File: emd_43612.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.28378528 - 0.58496565
Average (Standard dev.)0.0006256472 (±0.01556375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43612_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_43612_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_43612_half_map_2.map
AnnotationHalf 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 : Binary Complex of Bos taurus DHX36 bound to a DNA G-quadruplex

EntireName: Binary Complex of Bos taurus DHX36 bound to a DNA G-quadruplex
Components
  • Complex: Binary Complex of Bos taurus DHX36 bound to a DNA G-quadruplex
    • Protein or peptide: ATP-dependent DNA/RNA helicase DHX36
    • DNA: DNA (29-MER)

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Supramolecule #1: Binary Complex of Bos taurus DHX36 bound to a DNA G-quadruplex

SupramoleculeName: Binary Complex of Bos taurus DHX36 bound to a DNA G-quadruplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: ATP-dependent DNA/RNA helicase DHX36

MacromoleculeName: ATP-dependent DNA/RNA helicase DHX36 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 111.646938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGRGGRGRHP GHLKGREIGL WYAKKQGQKN KEAERQERAV VHMDERREEQ IVQLLHSVQT KNDKDEEAQI SWFAPEDHGY GTEAPAENK PNSVKNVEHQ AAAMINQEKR PFRIRDKYID RDSEYLLQEN EPDATLDQQL LEDLQKKKTD LRYIEMQRFR E KLPSYGMQ ...String:
GGRGGRGRHP GHLKGREIGL WYAKKQGQKN KEAERQERAV VHMDERREEQ IVQLLHSVQT KNDKDEEAQI SWFAPEDHGY GTEAPAENK PNSVKNVEHQ AAAMINQEKR PFRIRDKYID RDSEYLLQEN EPDATLDQQL LEDLQKKKTD LRYIEMQRFR E KLPSYGMQ KELVNMIDNH QVTVISGETG CGKTTQVTQF ILDNYIERGK GSACRIVCTQ PRRISAISVA ERVAAERAES CG NGNSTGY QIRLQSRLPR KQGSILYCTT GIILQWLQSD PHLSSVSHIV LDEIHERNLQ SDVLMTVVKD LLSYRPDLKV VLM SATLNA EKFSEYFGNC PMIHIPGFTF PVVEYLLEDI IEKIRYVPEQ KEHRSQFKKG FMQGHVNRQE KEEKEAIYKE RWPG YLREL RQRYSASTVD VVEMMDDEKV DLNLIAALIR YIVLEEEDGA ILVFLPGWDN ISTLHDLLMS QVMFKSDKFI IIPLH SLMP TVNQTQVFKR TPPGVRKIVI ATNIAETSIT IDDVVYVIDG GKIKETHFDT QNNISTMSAE WVSKANAKQR KGRAGR VQP GHCYHLYNSL RASLLDDYQL PEILRTPLEE LCLQIKILRL GGIAHFLSRL MDPPSNEAVL LSIKHLMELN ALDKQEE LT PLGVHLARLP VEPHIGKMIL FGALFCCLDP VLTIAASLSF KDPFVIPLGK EKVADARRKE LAKDTKSDHL TVVNAFKG W EKAKQRGFRY EKDYCWEYFL SSNTLQMLHN MKGQFAEHLL GAGFVSSRNP QDPESNINSD NEKIIKAVIC AGLYPKVAK IRLNLGKKRK MVKVYTKTDG VVAIHPKSVN VEQTEFNYNW LIYHLKMRTS SIYLYDCTEV SPYCLLFFGG DISIQKDNDQ ETIAVDEWI IFQSPARIAH LVKELRKELD ILLQEKIESP HPVDWKDTKS RDCAVLSAII DLIKTQEKAT PRNLPPRFQD G YYSPHHHH HHHH

UniProtKB: ATP-dependent DNA/RNA helicase DHX36

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Macromolecule #2: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.119831 KDa
SequenceString:
(DA)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DA) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DT)(DT) (DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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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

BufferpH: 7.5
Component:
ConcentrationName
0.8 (V/v) %Glycerol
25.0 mMHEPES-KOH
150.0 mMPotassium Chloride
0.5 mMTCEP
2.5 mMMagnesium Chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 215200
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5vhe

source_name: PDB, initial_model_type: experimental model

1xav

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8vx8:
Cryo-EM Structure of DHX36 bound to the cMyc DNA G-quadruplex, Class 1

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