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- PDB-28zm: Crystal structure of human DHX8 in complex with compound 21 and ADP -

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Basic information

Entry
Database: PDB / ID: 28zm
TitleCrystal structure of human DHX8 in complex with compound 21 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: 2.85 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)317,28264
Polymers311,1314
Non-polymers6,15260
Water8,431468
1
A: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,66721
Polymers77,7831
Non-polymers1,88420
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,51119
Polymers77,7831
Non-polymers1,72818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,12213
Polymers77,7831
Non-polymers1,34012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,98211
Polymers77,7831
Non-polymers1,19910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.660, 167.184, 137.124
Angle α, β, γ (deg.)90.000, 92.580, 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, 528 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.: 15 / 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.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-A1J1F / 2-naphthalen-2-ylsulfanylpyridine-3-carboxylic acid


Mass: 281.329 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
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: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS4 XE CdTe 4M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.85→136.99 Å / Num. obs: 69824 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 68.5 Å2 / CC1/2: 0.878 / Rmerge(I) obs: 0.348 / Rpim(I) all: 0.175 / Rrim(I) all: 0.391 / Net I/σ(I): 4.8 / Num. measured all: 350600 / Scaling rejects: 4311
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
2.85-2.915.12.1252296145010.3271.0422.3721.499.6
13.67-136.994.60.130286620.9810.0580.1169.299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASERphasing
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→136.99 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.374
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 3283 4.71 %RANDOM
Rwork0.2101 ---
obs0.212 69698 99.6 %-
Displacement parametersBiso max: 122.93 Å2 / Biso mean: 55.2 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--9.0214 Å20 Å25.5442 Å2
2--4.1531 Å20 Å2
3---4.8682 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.85→136.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19552 0 424 471 20447
Biso mean--61.59 42.8 -
Num. residues----2535
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6960SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3534HARMONIC5
X-RAY DIFFRACTIONt_it20389HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2779SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16162SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20389HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg27630HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion17.45
LS refinement shellResolution: 2.85→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3654 80 5.74 %
Rwork0.3014 1314 -
all0.3055 1394 -
obs--99.64 %
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)
10.5055-0.3034-0.43470.5270.0020.9234-0.126-0.0890.05460.02060.1209-0.0656-0.14030.04490.00510.12230.0303-0.0367-0.1399-0.025-0.123616.151820.60834.2435
20.0692-0.31760.51820.6054-0.18181.8477-0.077-0.10490.0178-0.03560.1479-0.04670.2496-0.19-0.07090.0985-0.06120.0335-0.14550.0525-0.120616.708-20.67644.5463
30.11010.2928-0.42780.2016-0.05411.3679-0.07690.0759-0.0656-0.02650.07110.0015-0.2166-0.10820.00580.23390.0704-0.0366-0.13580.0413-0.188815.641120.3668-63.9826
40.20840.30490.33650.46020.271.2172-0.10830.04-0.0408-0.01810.0367-0.04850.22290.11750.07150.23720.0610.0536-0.1639-0.01-0.179323.5862-20.2328-63.6185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A556 - 1186
2X-RAY DIFFRACTION2{ B|* }B556 - 1198
3X-RAY DIFFRACTION3{ C|* }C556 - 1188
4X-RAY DIFFRACTION4{ D|* }D556 - 1188

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