2026-10-14 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2026-03-05 2026-10-14 2026-10-14 2026-10-14 Cancer Research UK C309/A8274 and C309/A11566 United Kingdom Cryo-EM structure of human DHX9 in complex with ATX-968 and ADP. Hallett ST Silva STN Le Bihan Y Van Montfort R RNA helicase, RNA BINDING PROTEIN Read BJ Ewens C Gigante F Thomas J Felisberto-Rodrigues C Alvarez Peres S Tighe C de Las Heras Ruiz E Schiemann K Malcolm AG McAndrew PC Stubbs M Patani H Costa HDS Stoodley K Pickard L Busch M Gunnell E Silva S Knopp A Hallett ST Augustin M Lammens A Carter M Meniconi M Ballarotto M Ainsley J Meister P Sethi D Burke R Scarpino A Le Bihan YV Gradler U Blagg J Workman P Clarke PA Blum A Esdar C Bhalay G van Montfort RLM Fragment-Based Discovery of Potent RNA-Competitive Inhibitors of the DEAH-Box RNA Helicase DHX8. J.Med.Chem. US 69 18277 18299 2026 42593941 doi:10.1021/acs.jmedchem.6c00732 0022-2623 0151 JMCMAR 29by FULLOVERLAP EMDB EMD-57068 associated EM volume
Cryo-EM structure of human DHX9 in complex with ATX-968 and ADP.
 Human DHX9 bound to ATX-968 and ADP. Human DHX9 bound to ATX-968 and ADP. 0 1 Homo sapiens ATP-dependent RNA helicase A Homo sapiens 0.114340164 1 Spodoptera frugiperda LEVO MSRKEEQEVQATLESEEVDLNAGLHGNWTLENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFA REHGSNKKLAAQSCALSLVRQLYHLGVVEAYSGLTKKKEGETVEPYKVNLSQDLEHQLQNIIQELNLEILPPPEDPSVPV ALNIGKLAQFEPSQRQNQVGVVPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQLEQDHDLQAILQERELL PVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKS CGYSVRFESILPRPHASIMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDT SMFCEYFFNCPIIEVYGRTYPVQEYFLEDCIQMTHFVPPPKDKKKKDKDDDGGEDDDANCNLICGDEYGPETRLSMSQLN EKETPFELIEALLKYIETLNVPGAVLVFLPGWNLIYTMQKHLEMNPHFGSHRYQILPLHSQIPREEQRKVFDPVPVGVTK VILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRARFERLETH MTPEMFRTPLHEIALSIKLLRLGGIGQFLAKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLPIEPRFGKMM IMGCIFYVGDAICTIAAATCFPEPFINEGKRLGYIHRNFAGNRFSDHVALLSVFQAWDDARMGGEEAEIRFCEHKRLNMA TLRMTWEAKVQLKEILINSGFPEDCLLTQVFTNTGPDNNLDVVISLLAFGVYPNVCYHKEKRKILTTEGRNALIHKSSVN CPFSSQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFASKKVQSDGQIVLVDDWIKLQISHEAAACITGLRAAME ALVVEVTKQPAIISQLDPVNERMLNMIRQISRPSAAGINLMIDYKDDDDK Q08211 3.6.4.13 ADENOSINE-5'-DIPHOSPHATE 0.000427201 1 ADP MAGNESIUM ION 2.4305e-05 1 MG (4M)-N-[3-chloro-5-(methanesulfonamido)phenyl]-4-(3-methylpyridin-2-yl)thiophene-2-carboxamide 0.00042192099999999996 1 A1BKX water 1.8015e-05 22 HOH singleParticle particle 0.5 7.5
20 mM HEPES pH 7.5, 300 mM NaCl, 2 mM TCEP
 UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY 50.0 PLASMA CLEANING AIR
15 W
 ETHANE 100 277 FEI VITROBOT MARK IV
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..
Sample was fairly monodisperse.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.4 1.8 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20
Due to potential preferred particle orientation additional movies were collected from the same grid at a tilt of 30 degrees.
Preliminary grid screening was performed in a Glacios.
GATAN K3 BIOQUANTUM (6k x 4k) 1 35037 1.55 60.0
Images collected in movie mode (60 frames per movie).
 1 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION
Used internally produced model, obtained by X-ray crystallography, as starting model.
 2.8 FSC 0.143 CUT-OFF RELION 5.0 985972 MAXIMUM LIKELIHOOD RELION 5.0 MAXIMUM LIKELIHOOD RELION 5.0 RELION 5.0
Particles from CryoSPARC were re-extracted in RELION using a box size of 256 x 256 pixels with no downscaling. 3D auto-refinement was performed followed by per particle CTF refinement, another round of 3D auto-refinement and then Bayesian polishing. During polishing particles were extracted in a box size of 512 x 512 pixels downscaled to 256 x 256 pixels to maintain a pixel size of 1.017 Angstrom.
 emd_57068.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 260.352 260.352 260.352 90.0 90.0 90.0 X Y Z -0.06187148 0.094118185 0.00000575866 0.0015841502 1.017 1.017 1.017 0.012 AUTHOR Other experimental model
Model produced in-house by X-ray crystallography.
 OTHER
Initial fit was done in Chimera, followed by chain adjustments in Coot and refinement in Phenix.
REAL 64.980000000000004 emd_57068_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 260.352 260.352 260.352 90.0 90.0 90.0 X Y Z -0.021871923 0.04795077 0.0000061378423 0.0009640726 1.017 1.017 1.017 AUTHOR emd_57068_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 260.352 260.352 260.352 90.0 90.0 90.0 X Y Z -0.02200185 0.047010884 0.000005916474 0.0009632968 1.017 1.017 1.017 AUTHOR