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- PDB-28zj: Crystal structure of human DHX8 in complex with compound 4 and ADP -

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Basic information

Entry
Database: PDB / ID: 28zj
TitleCrystal structure of human DHX8 in complex with compound 4 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 / IBUPROFEN / (2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / ATP-dependent RNA helicase DHX8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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)319,69298
Polymers311,1314
Non-polymers8,56194
Water10,719595
1
A: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,76423
Polymers77,7831
Non-polymers1,98222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,96726
Polymers77,7831
Non-polymers2,18425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,11626
Polymers77,7831
Non-polymers2,33425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,84523
Polymers77,7831
Non-polymers2,06222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.232, 166.187, 137.337
Angle α, β, γ (deg.)90.000, 92.610, 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 , 8 types, 689 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.: 45 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-IBP / IBUPROFEN / 2-(4-ISOBUTYLPHENYL)PROPIONIC ACID


Mass: 206.281 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H18O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, medication*YM
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Chemical ChemComp-IZP / (2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / (R)-Ibuprofen


Mass: 206.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.55→49.01 Å / Num. obs: 95011 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.132 / Net I/σ(I): 7.3
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4716 / CC1/2: 0.309 / Rrim(I) all: 0.872 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
Aimless0.6.3data scaling
PHASERphasing
PDB_EXTRACT3.28data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→36.84 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.683 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.632 / SU Rfree Blow DPI: 0.278 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 4629 4.87 %RANDOM
Rwork0.2073 ---
obs0.2089 94964 98.5 %-
Displacement parametersBiso max: 125.28 Å2 / Biso mean: 56.4 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.034 Å20 Å22.0769 Å2
2---2.8414 Å20 Å2
3---2.8754 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.55→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19510 0 508 597 20615
Biso mean--74.06 50.03 -
Num. residues----2539
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6891SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3447HARMONIC5
X-RAY DIFFRACTIONt_it20365HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2781SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16851SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20365HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg27595HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion16.53
LS refinement shellResolution: 2.55→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3364 103 5.42 %
Rwork0.332 1797 -
all0.3322 1900 -
obs--99.57 %
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)
10.5222-0.2915-0.32490.4082-0.08060.8938-0.098-0.05590.02080.06490.0721-0.0546-0.16970.08170.0260.0248-0.0083-0.0529-0.0745-0.0162-0.076616.044321.17824.4084
20.1548-0.25130.37420.5199-0.13221.3956-0.0507-0.0668-0.0154-0.0010.1036-0.00570.1866-0.133-0.0529-0.0256-0.05580.0027-0.07680.0692-0.034516.6935-19.94064.7625
30.18890.3151-0.36160.4052-0.03551.2235-0.1060.0721-0.0711-0.05270.07160.0059-0.1803-0.09330.03440.08330.0227-0.0379-0.06140.0311-0.140815.647420.8527-64.4575
40.22340.28880.26450.44880.26651.3829-0.07970.0062-0.0362-0.06270.0346-0.06160.18020.10220.04510.05130.03120.0398-0.0992-0.0348-0.082223.3859-19.6404-63.9404
50.13660.1224-0.09110.16050.16020.37620.00230.00530.0596-0.0350.1143-0.1192-0.00060.0608-0.11650.00760.0172-0.0230.0508-0.07760.07717.2749-1.2618-35.6274
60.1356-0.13260.0950.03050.16630.4158-0.02450.10690.0090.0651-0.08330.03820.06220.01040.10780.062-0.0996-0.0383-0.04260.0157-0.132217.96110.8826-20.9662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|556 - A|1197 A|1301 - A|1304 }A556 - 1197
2X-RAY DIFFRACTION1{ A|556 - A|1197 A|1301 - A|1304 }A1301 - 1304
3X-RAY DIFFRACTION2{ B|556 - B|1198 B|1301 - B|1304 }B556 - 1198
4X-RAY DIFFRACTION2{ B|556 - B|1198 B|1301 - B|1304 }B1301 - 1304
5X-RAY DIFFRACTION3{ C|556 - C|1188 C|1301 - C|1305 }C556 - 1188
6X-RAY DIFFRACTION3{ C|556 - C|1188 C|1301 - C|1305 }C1301 - 1305
7X-RAY DIFFRACTION4{ D|556 - D|1188 D|1301 - D|1304 }D556 - 1188
8X-RAY DIFFRACTION4{ D|556 - D|1188 D|1301 - D|1304 }D1301 - 1304
9X-RAY DIFFRACTION5{ A|1305 - A|1312 B|1305 - B|1313 C|1307 - C|1317 D|1305 - D|1317 }A1305 - 1312
10X-RAY DIFFRACTION5{ A|1305 - A|1312 B|1305 - B|1313 C|1307 - C|1317 D|1305 - D|1317 }B1305 - 1313
11X-RAY DIFFRACTION5{ A|1305 - A|1312 B|1305 - B|1313 C|1307 - C|1317 D|1305 - D|1317 }C1307 - 1317
12X-RAY DIFFRACTION5{ A|1305 - A|1312 B|1305 - B|1313 C|1307 - C|1317 D|1305 - D|1317 }D1305 - 1317
13X-RAY DIFFRACTION6{ A|1313 - A|1322 B|1314 - B|1325 C|1318 - C|1325 D|1318 - D|1322 }A1313 - 1322
14X-RAY DIFFRACTION6{ A|1313 - A|1322 B|1314 - B|1325 C|1318 - C|1325 D|1318 - D|1322 }B1314 - 1325
15X-RAY DIFFRACTION6{ A|1313 - A|1322 B|1314 - B|1325 C|1318 - C|1325 D|1318 - D|1322 }C1318 - 1325
16X-RAY DIFFRACTION6{ A|1313 - A|1322 B|1314 - B|1325 C|1318 - C|1325 D|1318 - D|1322 }D1318 - 1322

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