EMDB-75038: Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961

Basic information

Entry

Database: EMDB / ID: EMD-75038

• Title: Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961
• Map data: final postprocess map

Sample

• Complex: Ternary complex of HBS1L, cereblon, and DDB1 with TNG961
  • Protein or peptide: HBS1-like protein
  • Protein or peptide: Protein cereblon
  • Protein or peptide: DNA damage-binding protein 1
• Ligand: N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea
• Ligand: ZINC ION

• Keywords: FOCAD / ribosome / PELO / ubiquitin / CYTOSOLIC PROTEIN

Function / homology

Function:

Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / mRNA decay by 3' to 5' exoribonuclease / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / ribosome disassembly / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / limb development / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / translation elongation factor activity / positive regulation of Wnt signaling pathway / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / proteasomal protein catabolic process / rescue of stalled cytosolic ribosome / positive regulation of gluconeogenesis / cytosolic ribosome / nucleotide-excision repair / sperm end piece / positive regulation of protein-containing complex assembly / regulation of circadian rhythm / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / regulation of translation / site of double-strand break / sperm principal piece / Neddylation / sperm midpiece / Potential therapeutics for SARS / ubiquitin-dependent protein catabolic process / damaged DNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / transmembrane transporter binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromosome, telomeric region / protein ubiquitination / translation / DNA repair / GTPase activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / GTP binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / signal transduction / protein-containing complex / : / DNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytoplasm / cytosol

Domain/homology:

HBS1-like protein, N-terminal domain superfamily / HBS1-like protein, N-terminal / HBS1 N-terminus / : / GTP-eEF1A C-terminal domain-like / : / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / PUA-like superfamily / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase

Component:

DNA damage-binding protein 1 / Protein cereblon / HBS1-like protein

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 2.9 Å
• Authors: Whittington DA

Funding support

1 items

Organization	Grant number	Country
Other private

• Citation: Journal: Cancer Discov / Year: 2026; Title: TNG961 is a selective oral HBS1L molecular glue degrader for the treatment of FOCAD-deleted cancers.; Authors: Hilary E Nicholson / Douglas A Whittington / Frank J Bruzzese / Katherine Lazarides / Lauren Catherine M Martires / Matthew R Tonini / Helena N Jenkins / Minjie Zhang / Preksha Shahagadkar / Charlotte B Pratt / Kimberly J Briggs / Patrick McCarren / Alice Tsai / Madhavi Bandi / Chengyin Min / Alan Huang / Hongxiang Zhang / Samuel R Meier / Binzhang Shen / Yi Yu / Colin Liang / Yong Liu / Teng Teng / John Zhang / Adam Crystal / William D Mallender / Xinyuan Edward Wu / John P Maxwell / Jannik N Andersen / ; Abstract: When tumor suppressor genes are lost through chromosomal deletion, deletion of adjacent genes can generate therapeutic vulnerabilities. MTAP is frequently co-deleted with the Chr9p21 tumor suppressor gene CDKN2A, creating synthetic lethal dependency on PRMT5. Telomeric to MTAP lies FOCAD, whose loss induces dependency on the HBS1L/PELO ribosome-rescue complex for translational maintenance. FOCAD is deleted in ~1/3 of MTAP-deleted cancers. We screened an IMiD-focused diversity library and identified a weak hit that bound cereblon, promoted HBS1L-CRBN-compound complex formation, and induced E3-ligase-dependent HBS1L ubiquitination and degradation. Guided by cryo-EM structures and proteome selectivity we developed TNG961, a potent, selective HBS1L degrader that disrupts the HBS1L/PELO complex, inducing translational arrest, unfolded protein response activation, and growth inhibition in FOCAD-negative models. Oral administration of TNG961 regresses FOCAD-negative xenografts, including PRMT5 inhibitor-refractory models, establishing HBS1L degradation as a strategy to exploit FOCAD loss and supporting clinical evaluation of TNG961 as a first-in-class precision oncology therapeutic.

History

Deposition	Jan 9, 2026	-
Header (metadata) release	Apr 22, 2026	-
Map release	Apr 22, 2026	-
Update	May 6, 2026	-
Current status	May 6, 2026	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_75038.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: final postprocess map
• Voxel size: X=Y=Z: 0.932 Å

Density

Contour Level	By AUTHOR: 0.01
Minimum - Maximum	-0.04023661 - 0.067853495
Average (Standard dev.)	0.000015975365 (±0.0017226402)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 335.52 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_75038_msk_1.map

Half map: Half map 1

• File: emd_75038_half_map_1.map
• Annotation: Half map 1

Half map: Half map 2

• File: emd_75038_half_map_2.map
• Annotation: Half map 2

Sample components

Entire : Ternary complex of HBS1L, cereblon, and DDB1 with TNG961

• Entire: Name: Ternary complex of HBS1L, cereblon, and DDB1 with TNG961

Components

• Complex: Ternary complex of HBS1L, cereblon, and DDB1 with TNG961
  • Protein or peptide: HBS1-like protein
  • Protein or peptide: Protein cereblon
  • Protein or peptide: DNA damage-binding protein 1
• Ligand: N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea
• Ligand: ZINC ION

Supramolecule #1: Ternary complex of HBS1L, cereblon, and DDB1 with TNG961

• Supramolecule: Name: Ternary complex of HBS1L, cereblon, and DDB1 with TNG961; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 393 KDa

Macromolecule #1: HBS1-like protein

• Macromolecule: Name: HBS1-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO; EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 22.94701 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GKPPQRSIDK PFRLCVSDVF KDQGSGFCIT GKIEAGYIQT GDRLLAMPPN ETCTVKGITL HDEPVDWAAA GDHVSLTLVG MDIIKINVG CIFCGPKVPI KACTRFRARI LIFNIEIPIT KGFPVLLHYQ TVSEPAVIKR LISVLNKSTG EVTKKKPKFL T KGQNALVE LQTQRPIALE LYKDFKELGR FMLRYGGSTI AAGVVTEIKE

UniProtKB: HBS1-like protein

Macromolecule #2: Protein cereblon

• Macromolecule: Name: Protein cereblon / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 46.378293 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

GEAKKPNIIN FDTSLPTSHT YLGADMEEFH GRTLHDDDSC QVIPVLPQVM MILIPGQTLP LQLFHPQEVS MVRNLIQKDR TFAVLAYSN VQEREAQFGT TAEIYAYREE QDFGIEIVKV KAIGRQRFKV LELRTQSDGI QQAKVQILPE CVLPSTMSAV Q LESLNKCQ IFPSKPVSRE DQCSYKWWQK YQKRKFHCAN LTSWPRWLYS LYDAETLMDR IKKQLREWDE NLKDDSLPSN PI DFSYRVA ACLPIDDVLR IQLLKIGSAI QRLRCELDIM NKCTSLCCKQ CQETEITTKN EIFSLSLCGP MAAYVNPHGY VHE TLTVYK ACNLNLIGRP STEHSWFPGY AWTVAQCKIC ASHIGWKFTA TKKDMSPQKF WGLTRSALLP TIPDTEDEIS PDKV ILCL

UniProtKB: Protein cereblon

Macromolecule #3: DNA damage-binding protein 1

• Macromolecule: Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 127.097469 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

Macromolecule #4: N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(tri...

• Macromolecule: Name: N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea; type: ligand / ID: 4 / Number of copies: 2 / Formula: A1C4S
• Molecular weight: Theoretical: 539.569 Da

Macromolecule #5: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 8 mg/mL
• Buffer: pH: 7.5 ; Details: 0.1 M HEPES (pH 7.5), 0.24 M sodium chloride, 3 mM TCEP, 0.2 % n-octylglucoside
• Grid: Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
• Details: sample kept at 4 degrees Celsius

Electron microscopy

• Microscope: TFS KRIOS
• Specialist optics: Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
• Image recording: Film or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 9532 / Average electron dose: 48.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 4475226
• CTF correction: Software - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: OTHER / Details: Ab initio reconstruction
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 669259
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD
• Final 3D classification: Number classes: 5 / Software - Name: RELION (ver. 5.0)

Atomic model buiding 1

Initial model

PDB ID	Chain	Details
5hxb	chain_id: B, source_name: PDB, initial_model_type: experimental model
5hxb	chain_id: C, source_name: PDB, initial_model_type: experimental model
	source_name: Other, initial_model_type: experimental model	proprietary HBS1L crystal structure

• Details: rigid body placement of proteins followed by real space refinement
• Refinement: Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient

Output model

PDB-10ay:
Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961