[English] 日本語
Yorodumi
- PDB-29by: Cryo-EM structure of human DHX9 in complex with ATX-968 and ADP. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29by
TitleCryo-EM structure of human DHX9 in complex with ATX-968 and ADP.
ComponentsATP-dependent RNA helicase A
KeywordsRNA BINDING PROTEIN / RNA helicase
Function / homology
Function and homology information


single-stranded 3'-5' DNA helicase activity / 3'-5' DNA/RNA helicase activity / regulatory region RNA binding / CRD-mediated mRNA stability complex / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / G-quadruplex unwinding activity / regulation of cytoplasmic translation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...single-stranded 3'-5' DNA helicase activity / 3'-5' DNA/RNA helicase activity / regulatory region RNA binding / CRD-mediated mRNA stability complex / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / G-quadruplex unwinding activity / regulation of cytoplasmic translation / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RISC complex binding / CRD-mediated mRNA stabilization / triplex DNA binding / importin-alpha family protein binding / nucleoside triphosphate diphosphatase activity / protein localization to cytoplasmic stress granule / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / alternative mRNA splicing, via spliceosome / positive regulation of interleukin-18 production / nuclear stress granule / perichromatin fibrils / 3'-5' RNA helicase activity / miRNA-mediated post-transcriptional gene silencing / regulation of defense response to virus by host / regulation of mRNA processing / RISC-loading complex / positive regulation of response to cytokine stimulus / RIP-mediated NFkB activation via ZBP1 / RISC complex assembly / siRNA binding / positive regulation of cytoplasmic translation / sequence-specific mRNA binding / RNA polymerase binding / RISC complex / RNA stem-loop binding / positive regulation of innate immune response / cellular response to exogenous dsRNA / positive regulation of interferon-alpha production / RNA polymerase II complex binding / DNA replication origin binding / pyroptotic inflammatory response / 3'-5' DNA helicase activity / mRNA Splicing - Major Pathway / positive regulation of interferon-beta production / positive regulation of fibroblast proliferation / positive regulation of DNA replication / positive regulation of DNA repair / promoter-specific chromatin binding / chromatin DNA binding / positive regulation of interleukin-6 production / osteoblast differentiation / PKR-mediated signaling / transcription coregulator activity / mRNA Polyadenylation / cytoplasmic ribonucleoprotein granule / positive regulation of inflammatory response / actin cytoskeleton / positive regulation of tumor necrosis factor production / double-stranded RNA binding / single-stranded DNA binding / ribonucleoside triphosphate phosphatase activity / ribosome binding / chromatin organization / protein-containing complex assembly / Dengue Virus-Host Interactions / double-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / DNA helicase activity / transcription coactivator activity / RNA helicase activity / single-stranded RNA binding / ribonucleoprotein complex / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mRNA binding / centrosome / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-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 ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-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 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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
: / ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / MOLECULAR REPLACEMENT / molecular replacement / cryo EM / Resolution: 2.8 Å
AuthorsHallett, S.T. / Silva, S.T.N. / Le Bihan, Y. / Van Montfort, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC309/A8274 and C309/A11566 United Kingdom
CitationJournal: J Med Chem / Year: 2026
Title: Fragment-Based Discovery of Potent RNA-Competitive Inhibitors of the DEAH-Box RNA Helicase DHX8.
Authors: Benjamin J Read / Caroline Ewens / Federica Gigante / Jemima Thomas / Catarina Felisberto-Rodrigues / Silvia Alvarez Peres / Catherine Tighe / Edgar de Las Heras Ruiz / Kai Schiemann / ...Authors: Benjamin J Read / Caroline Ewens / Federica Gigante / Jemima Thomas / Catarina Felisberto-Rodrigues / Silvia Alvarez Peres / Catherine Tighe / Edgar de Las Heras Ruiz / Kai Schiemann / Andrew G Malcolm / Peter Craig McAndrew / Mark Stubbs / Harshnira Patani / Helena Dos Santos Costa / Katharine Stoodley / Lisa Pickard / Michael Busch / Emma Gunnell / Sara Silva / Alexandra Knopp / Stephen T Hallett / Martin Augustin / Alfred Lammens / Michael Carter / Mirco Meniconi / Marco Ballarotto / Jon Ainsley / Paul Meister / Debarati Sethi / Rosemary Burke / Andrea Scarpino / Yann-Vaï Le Bihan / Ulrich Grädler / Julian Blagg / Paul Workman / Paul A Clarke / Andreas Blum / Christina Esdar / Gurdip Bhalay / Rob L M van Montfort /
Abstract: Human DHX8 is a spliceosomal DEAH-box RNA helicase involved in releasing mRNA from the spliceosome and crucial in ensuring splicing fidelity. DHX8 was identified as a promising therapeutic oncology ...Human DHX8 is a spliceosomal DEAH-box RNA helicase involved in releasing mRNA from the spliceosome and crucial in ensuring splicing fidelity. DHX8 was identified as a promising therapeutic oncology target due to its role in regulating stress-adaptive gene expression, including HSF1-dependent transcription, while having broader transcriptional effects in cells under oncogenic stress. We report the discovery of novel RNA-competitive DHX8 inhibitors based on a 2-(phenethylthio)nicotinic acid scaffold, which were optimized using a structure-guided design approach, following a biophysical fragment screen. This yielded compound 53 with nanomolar biochemical potency, good in vitro PK, and activity in a cellular target engagement assay. Optimizing inhibitor binding between Arg647 and the nonconserved His693, coupled with extending into a pocket in the DHX8 Winged-Helix domain, was crucial for potency improvement. By binding in the Winged-Helix domain, these inhibitors restrict the helicase domain's conformational plasticity, stabilizing a closed, inactive conformation while sterically blocking ssRNA translocation.
History
DepositionMar 5, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent RNA helicase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2144
Polymers114,3401
Non-polymers8733
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Monomer by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ATP-dependent RNA helicase A / DEAH box protein 9 / DExH-box helicase 9 / Leukophysin / LKP / Nuclear DNA helicase II / NDH II / ...DEAH box protein 9 / DExH-box helicase 9 / Leukophysin / LKP / Nuclear DNA helicase II / NDH II / RNA helicase A


Mass: 114340.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX9, DDX9, LKP, NDH2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08211, RNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1BKX / (4M)-N-[3-chloro-5-(methanesulfonamido)phenyl]-4-(3-methylpyridin-2-yl)thiophene-2-carboxamide


Mass: 421.921 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16ClN3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human DHX9 bound to ATX-968 and ADP. / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES pH 7.5, 300 mM NaCl, 2 mM TCEP
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was fairly monodisperse.
Specimen supportDetails: 15 W / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Sample was centrifuged at 21,000 x g for 10 minutes at 6 degrees Celsius and diluted to 0.5 mg/mL (4.34 micromolar) just before grid preparation. 3 microlitres of the sample was applied to ...Details: Sample was centrifuged at 21,000 x g for 10 minutes at 6 degrees Celsius and diluted to 0.5 mg/mL (4.34 micromolar) just before grid preparation. 3 microlitres of the sample was applied to the grid, blotted for 3 seconds with a blot force of 3, and immediately flash frozen.
CrystalMosaicity: 0 °

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Preliminary grid screening was performed in a Glacios.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.55 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 35037
Details: Images collected in movie mode (60 frames per movie).
EM imaging opticsEnergyfilter name: GIF Bioquantum
Details: Due to potential preferred particle orientation additional movies were collected from the same grid at a tilt of 30 degrees.
Energyfilter slit width: 20 eV
ReflectionResolution: 3.4→49.73 Å / Num. obs: 81625 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.042 / Rrim(I) all: 0.157 / Net I/σ(I): 11.8 / Num. measured all: 1106095 / Scaling rejects: 1138
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.46143.6126167544120.50.9943.7471100
17.67-49.7311.40.02674316500.9940.0080.02769.795.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.0particle selectionParticle picking was first performed using Blob Picker to generate initial 2D classes
2EPU3.4image acquisition
4CTFFIND4.1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 985972 / Symmetry type: POINT
Atomic model buildingB value: 64.98 / Protocol: OTHER / Space: REAL
Details: Initial fit was done in Chimera, followed by chain adjustments in Coot and refinement in Phenix.
Atomic model buildingDetails: Model produced in-house by X-ray crystallography. / Source name: Other / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cross valid method: THROUGHOUT
Displacement parametersBiso max: 125.82 Å2 / Biso mean: 64.5121 Å2 / Biso min: 17.76 Å2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more