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- PDB-8vvd: Cryo-EM Structure of DHX36 bound to a RNA G-quadruplex derived fr... -

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Basic information

Entry
Database: PDB / ID: 8vvd
TitleCryo-EM Structure of DHX36 bound to a RNA G-quadruplex derived from the cMyc G-quadruplex, Class 2
Components
  • ATP-dependent DNA/RNA helicase DHX36
  • RNA (27-MER)
KeywordsMOTOR PROTEIN/RNA / DEAH-Box Helicase / Helicase / G-quadruplex / RNA / MOTOR PROTEIN / MOTOR PROTEIN-RNA complex
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 / G-quadruplex RNA binding / perikaryon / 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 / cytoplasm / cytosol
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
RNA / RNA (> 10) / ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsBanco, M.T. / Ferre-D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Inter-domain synergy enables both DNA and RNA G-quadruplex unwinding by the DEAH-box helicase DHX36
Authors: Banco, M.T. / Paul, T. / Jiang, J. / Myong, S. / Ferre-D'Amare, A.R.
History
DepositionJan 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA/RNA helicase DHX36
B: RNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)120,4222
Polymers120,4222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ATP-dependent DNA/RNA helicase DHX36 / DEAD/H box polypeptide 36 / DEAH-box protein 36 / G4-resolvase-1 / G4R1 / MLE-like protein 1 / RNA ...DEAD/H box polypeptide 36 / DEAH-box protein 36 / G4-resolvase-1 / G4R1 / MLE-like protein 1 / RNA helicase associated with AU-rich element protein


Mass: 111646.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: DHX36 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05B79, DNA helicase, RNA helicase
#2: RNA chain RNA (27-MER)


Mass: 8775.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: Binary Complex of Bos taurus DHX36 bound to a RNA construct derived from the cMyc G-quadruplex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bos taurus (domestic cattle)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
10.8 (V/v) %Glycerol1
225 mMHEPES-KOH1
3150 mMPotassium Chloride1
40.5 mMTCEP1
52.5 mMMagnesium Chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameCategory
1RELIONparticle selection
4RELIONCTF correction
7PHENIXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103273 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5VHE

5vhe


Accession code: 5VHE / Source name: PDB / Type: experimental model

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