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- PDB-9mfo: Human DHX9 in Complex with Compound 1 and ADP -

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Basic information

Entry
Database: PDB / ID: 9mfo
TitleHuman DHX9 in Complex with Compound 1 and ADP
ComponentsATP-dependent RNA helicase A
KeywordsHYDROLASE / Helicase / DHX9 / Inhibitor / Complex
Function / homology
Function and homology information


catalytic activity, acting on a nucleic acid / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / regulation of cytoplasmic translation / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / triplex DNA binding ...catalytic activity, acting on a nucleic acid / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / regulation of cytoplasmic translation / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / triplex DNA binding / RISC complex binding / CRD-mediated mRNA stabilization / nucleoside triphosphate diphosphatase activity / protein localization to cytoplasmic stress granule / importin-alpha family protein binding / perichromatin fibrils / positive regulation of interleukin-18 production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / nuclear stress granule / 3'-5' RNA helicase activity / alternative mRNA splicing, via spliceosome / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / regulation of mRNA processing / RISC complex assembly / regulation of defense response to virus by host / positive regulation of response to cytokine stimulus / RIP-mediated NFkB activation via ZBP1 / siRNA binding / positive regulation of cytoplasmic translation / RISC complex / positive regulation of innate immune response / sequence-specific mRNA binding / RNA polymerase binding / 3'-5' DNA helicase activity / pyroptotic inflammatory response / cellular response to exogenous dsRNA / RNA polymerase II complex binding / positive regulation of interferon-alpha production / DNA replication origin binding / mRNA transport / DNA helicase activity / mRNA Splicing - Major Pathway / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / positive regulation of DNA repair / positive regulation of DNA replication / transcription coregulator activity / promoter-specific chromatin binding / DNA-templated transcription termination / PKR-mediated signaling / chromatin DNA binding / positive regulation of interleukin-6 production / cytoplasmic ribonucleoprotein granule / RNA stem-loop binding / positive regulation of inflammatory response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / osteoblast differentiation / rhythmic process / actin cytoskeleton / single-stranded DNA binding / double-stranded RNA binding / chromatin organization / ribosome binding / protein-containing complex assembly / double-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / single-stranded 3'-5' DNA helicase activity / transcription coactivator activity / DNA replication / single-stranded RNA binding / RNA helicase activity / nuclear body / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ribonucleoprotein complex / innate immune response / mRNA binding / centrosome / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsLockbaum, G.J. / Lee, Y.-T. / Sickmier, E.A. / Boriack-Sjodin, P.A. / Grigoriu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of ATX968: An Orally Available Allosteric Inhibitor of DHX9.
Authors: Daniels, M.H. / Castro, J. / Lee, Y.T. / Gotur, D. / Knockenhauer, K.E. / Grigoriu, S. / Lockbaum, G.J. / Cheong, J.E. / Lu, C. / Brennan, D. / Buker, S.M. / Liu, J. / Yao, S. / Sparling, B. ...Authors: Daniels, M.H. / Castro, J. / Lee, Y.T. / Gotur, D. / Knockenhauer, K.E. / Grigoriu, S. / Lockbaum, G.J. / Cheong, J.E. / Lu, C. / Brennan, D. / Buker, S.M. / Liu, J. / Yao, S. / Sparling, B.A. / Sickmier, E.A. / Ribich, S. / Blakemore, S.J. / Silver, S.J. / Boriack-Sjodin, P.A. / Duncan, K.W. / Copeland, R.A.
History
DepositionDec 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,4988
Polymers114,3401
Non-polymers1,1587
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.520, 85.520, 350.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1312-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 / Fragment: residues 150-1150
Source method: isolated from a genetically manipulated source
Details: Monomeric / Source: (gene. exp.) Homo sapiens (human) / Gene: DHX9, DDX9, LKP, NDH2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08211, RNA helicase

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Non-polymers , 5 types, 40 molecules

#2: Chemical ChemComp-A1BK0 / 1-ethyl-N-[3-(methanesulfonamido)phenyl]-5-methyl-1H-pyrazole-3-carboxamide


Mass: 322.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate, 0.1 M MES pH 6, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.26→38.46 Å / Num. obs: 20314 / % possible obs: 99.81 % / Redundancy: 25 % / CC1/2: 0.999 / Rmerge(I) obs: 0.182 / Net I/σ(I): 15.5
Reflection shellResolution: 3.26→3.345 Å / Redundancy: 26.4 % / Rmerge(I) obs: 2.019 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1435 / CC1/2: 0.781 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata processing
XDSdata scaling
Aimlessdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→38.46 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 30.397 / SU ML: 0.472 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28825 1024 4.8 %RANDOM
Rwork0.23572 ---
obs0.23815 20314 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.277 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å20 Å2
2--2.17 Å2-0 Å2
3----4.35 Å2
Refinement stepCycle: 1 / Resolution: 3.26→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6817 0 70 33 6920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137038
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156754
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.6479557
X-RAY DIFFRACTIONr_angle_other_deg0.9921.57415558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7385858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9522.445364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.992151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8471547
X-RAY DIFFRACTIONr_chiral_restr0.0320.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.05313.1723441
X-RAY DIFFRACTIONr_mcbond_other3.05313.1713440
X-RAY DIFFRACTIONr_mcangle_it5.22619.7554296
X-RAY DIFFRACTIONr_mcangle_other5.22519.7564297
X-RAY DIFFRACTIONr_scbond_it2.47513.5043597
X-RAY DIFFRACTIONr_scbond_other2.46713.4973578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.42720.1435238
X-RAY DIFFRACTIONr_long_range_B_refined7.9877406
X-RAY DIFFRACTIONr_long_range_B_other7.9877407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.26→3.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 93 -
Rwork0.362 1435 -
obs--99.8 %

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