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- PDB-28zo: Crystal structure of human DHX8 in complex with compound 24 and ADP -

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Basic information

Entry
Database: PDB / ID: 28zo
TitleCrystal structure of human DHX8 in complex with compound 24 and ADP
ComponentsATP-dependent RNA helicase DHX8
KeywordsRNA BINDING PROTEIN / Helicase / RNA / Splicing / Inhibitor / Cancer
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / U2-type catalytic step 2 spliceosome / RNA processing / catalytic step 2 spliceosome / spliceosomal complex / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase ...ATP-dependent activity, acting on RNA / U2-type catalytic step 2 spliceosome / RNA processing / catalytic step 2 spliceosome / spliceosomal complex / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
DHX8/ Prp22, 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 ...DHX8/ Prp22, 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / S1 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 / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase DHX8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.97 Å
AuthorsFelisberto-Rodrigues, C. / Silva, S.T.N. / Le Bihan, Y.-V. / van Montfort, R.L.M.
Funding support United Kingdom, Germany, 3items
OrganizationGrant numberCountry
Cancer Research UKC309/A8274 United Kingdom
Cancer Research UKC309/A11566 United Kingdom
Other private Germany
CitationJournal: J.Med.Chem. / Year: 2026
Title: Fragment-Based Discovery of Potent RNA-Competitive Inhibitors of the DEAH-Box RNA Helicase DHX8.
Authors: Read, B.J. / Ewens, C. / Gigante, F. / Thomas, J. / Felisberto-Rodrigues, C. / Alvarez Peres, S. / Tighe, C. / de Las Heras Ruiz, E. / Schiemann, K. / Malcolm, A.G. / McAndrew, P.C. / ...Authors: Read, B.J. / Ewens, C. / Gigante, F. / Thomas, J. / Felisberto-Rodrigues, C. / Alvarez Peres, S. / Tighe, C. / de Las Heras Ruiz, E. / Schiemann, K. / Malcolm, A.G. / McAndrew, P.C. / Stubbs, M. / Patani, H. / Costa, H.D.S. / Stoodley, K. / Pickard, L. / Busch, M. / Gunnell, E. / Silva, S. / Knopp, A. / Hallett, S.T. / Augustin, M. / Lammens, A. / Carter, M. / Meniconi, M. / Ballarotto, M. / Ainsley, J. / Meister, P. / Sethi, D. / Burke, R. / Scarpino, A. / Le Bihan, Y.V. / Gradler, U. / Blagg, J. / Workman, P. / Clarke, P.A. / Blum, A. / Esdar, C. / Bhalay, G. / van Montfort, R.L.M.
History
DepositionMar 3, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DHX8
B: ATP-dependent RNA helicase DHX8
C: ATP-dependent RNA helicase DHX8
D: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,37151
Polymers311,1314
Non-polymers5,24147
Water5,188288
1
A: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,52119
Polymers77,7831
Non-polymers1,73818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,89810
Polymers77,7831
Non-polymers1,1159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,89810
Polymers77,7831
Non-polymers1,1159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,05412
Polymers77,7831
Non-polymers1,27211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.881, 167.127, 137.101
Angle α, β, γ (deg.)90.000, 92.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ATP-dependent RNA helicase DHX8 / DEAH box protein 8 / RNA helicase HRH1


Mass: 77782.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX8, DDX8 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14562, RNA helicase

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Non-polymers , 6 types, 335 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-A1J1G / 2-(2-phenylethylsulfanyl)pyridine-3-carboxylic acid


Mass: 259.324 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.5 microliter of DHX8del547 at 3 mg/mL with 1 mM ADP and 1 mM MgCl2, plus 1.5 microliter of a crystallisation solution consisting of 15% (v/v) MPD, 100 mM Sodium Acetate pH 5.5 and 6% (v/v) ...Details: 0.5 microliter of DHX8del547 at 3 mg/mL with 1 mM ADP and 1 mM MgCl2, plus 1.5 microliter of a crystallisation solution consisting of 15% (v/v) MPD, 100 mM Sodium Acetate pH 5.5 and 6% (v/v) DMSO, against 250 microliter of crystallisation solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.97→167.13 Å / Num. obs: 62064 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 75.24 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.104 / Rrim(I) all: 0.237 / Net I/σ(I): 5.4 / Num. measured all: 315672 / Scaling rejects: 204
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
2.97-3.055.20.9042423046430.3110.4351.0051.4100
13.28-167.134.70.06734487260.9820.0390.07816.299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHASERphasing
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→136.97 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.412
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 3071 4.95 %RANDOM
Rwork0.2139 ---
obs0.2158 62036 100 %-
Displacement parametersBiso max: 115.49 Å2 / Biso mean: 66.28 Å2 / Biso min: 16.77 Å2
Baniso -1Baniso -2Baniso -3
1--11.7877 Å20 Å21.5402 Å2
2--3.3329 Å20 Å2
3---8.4548 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.97→136.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19482 0 324 288 20094
Biso mean--68.11 43.36 -
Num. residues----2537
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6885SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3460HARMONIC5
X-RAY DIFFRACTIONt_it20234HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2782SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16083SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20234HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg27457HARMONIC20.86
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion17
LS refinement shellResolution: 2.97→2.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3867 64 5.16 %
Rwork0.3415 1177 -
all0.3437 1241 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6145-0.2343-0.34710.5826-0.01111.1969-0.0933-0.0641-0.02450.03690.0839-0.0452-0.23180.07420.00940.0259-0.0187-0.0802-0.1429-0.0085-0.090316.408720.72954.2183
20.2997-0.15850.51320.7862-0.17661.7835-0.0586-0.07970.0167-0.02470.1128-0.03080.2377-0.1445-0.0541-0.0391-0.0440.0136-0.15430.0443-0.054516.8282-20.76554.7537
30.34430.2195-0.380.56630.04211.4258-0.08810.0787-0.1216-0.02740.0506-0.0336-0.2055-0.08360.03750.1101-0.0062-0.0618-0.15180.0174-0.157415.777420.3693-64.2271
40.31570.22990.29480.66430.391.203-0.03120.0114-0.0171-0.05150.0175-0.04440.15950.11680.01380.07510.01670.0143-0.1371-0.0197-0.118123.4997-20.3906-63.9278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A556 - 1187
2X-RAY DIFFRACTION2{ B|* }B556 - 1198
3X-RAY DIFFRACTION3{ C|* }C556 - 1188
4X-RAY DIFFRACTION4{ D|* }D556 - 1189

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