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- EMDB-70791: Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70791
TitleCryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex
Map data
Sample
  • Complex: DDB1/CRBN-MRT-5702-G3BP2 ternary complex
    • Protein or peptide: Protein cereblon
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Ras GTPase-activating protein-binding protein 2
  • Ligand: ZINC ION
  • Ligand: (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide
Keywordsmolecular glue degrader / neo-substrate / cereblon / E3 ubiquitin ligase / LIGASE
Function / homology
Function and homology information


: / positive regulation of stress granule assembly / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding ...: / positive regulation of stress granule assembly / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / 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 / mRNA transport / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / proteasomal protein catabolic process / positive regulation of gluconeogenesis / stress granule assembly / nucleotide-excision repair / molecular condensate scaffold activity / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / protein homooligomerization / regulation of circadian rhythm / 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 / Formation of Incision Complex in GG-NER / Wnt signaling pathway / cytoplasmic stress granule / 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 / site of double-strand break / signaling receptor complex adaptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / Ras protein signal transduction / chromosome, telomeric region / protein ubiquitination / innate immune response / DNA repair / mRNA binding / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
G3BP2, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. ...G3BP2, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / 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 / PUA-like superfamily / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / Protein cereblon / Ras GTPase-activating protein-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsQuan C / Petzold G / Gainza P / Tsai J / Bunker RD / Wiedmer L / Donckele EJ
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2026
Title: Cereblon induces G3BP2 neosubstrate degradation using molecular surface mimicry
Authors: Annunziato S / Quan C / Donckele EJ / Lamberto I / Bunker RD / Zlotosch M / Schwander L / Murthy A / Wiedmer L / Staehly C / Matysik M / Gilberto S / Kapsitidou D / Wible D / de Donatis GD / ...Authors: Annunziato S / Quan C / Donckele EJ / Lamberto I / Bunker RD / Zlotosch M / Schwander L / Murthy A / Wiedmer L / Staehly C / Matysik M / Gilberto S / Kapsitidou D / Wible D / de Donatis GD / Trenh P / SriRamaratnam R / Strande V / Almeida R / Dolgikh E / DeMarco B / Tsai J / Sadok A / Zarayskiy V / Walter M / Tiedt R / Lumb KJ / Bonenfant D / Fasching B / Castle JC / Townson SA / Petzold G / Gainza P
History
DepositionMay 23, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70791.png

Downloads & links

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Map

FileDownload / File: emd_70791.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 600 pix.
= 392.4 Å		0.65 Å/pix.
x 600 pix.
= 392.4 Å		0.65 Å/pix.
x 600 pix.
= 392.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.044
Minimum - Maximum-0.27231437 - 0.4863657
Average (Standard dev.)-0.00018413516 (±0.005867048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 392.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70791_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70791_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : DDB1/CRBN-MRT-5702-G3BP2 ternary complex

EntireName: DDB1/CRBN-MRT-5702-G3BP2 ternary complex
Components
  • Complex: DDB1/CRBN-MRT-5702-G3BP2 ternary complex
    • Protein or peptide: Protein cereblon
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Ras GTPase-activating protein-binding protein 2
  • Ligand: ZINC ION
  • Ligand: (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide

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Supramolecule #1: DDB1/CRBN-MRT-5702-G3BP2 ternary complex

SupramoleculeName: DDB1/CRBN-MRT-5702-G3BP2 ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.55409 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: INFDTSLPTS HTYLGADMEE FHGRTLHDDD SCQVIPVLPQ VMMILIPGQT LPLQLFHPQE VSMVRNLIQK DRTFAVLAYS NVQEREAQF GTTAEIYAYR EEQDFGIEIV KVKAIGRQRF KVLELRTQSD GIQQAKVQIL PECVLPSTMS AVQLESLNKC Q IFPSKPVS ...String:
INFDTSLPTS HTYLGADMEE FHGRTLHDDD SCQVIPVLPQ VMMILIPGQT LPLQLFHPQE VSMVRNLIQK DRTFAVLAYS NVQEREAQF GTTAEIYAYR EEQDFGIEIV KVKAIGRQRF KVLELRTQSD GIQQAKVQIL PECVLPSTMS AVQLESLNKC Q IFPSKPVS REDQCSYKWW QKYQKRKFHC ANLTSWPRWL YSLYDAETLM DRIKKQLREW DENLKDDSLP SNPIDFSYRV AA CLPIDDV LRIQLLKIGS AIQRLRCELD IMNKCTSLCC KQCQETEITT KNEIFSLSLC GPMAAYVNPH GYVHETLTVY KAC NLNLIG RPSTEHSWFP GYAWTVAQCK ICASHIGWKF TATKKDMSPQ KFWGLTRSAL LP

UniProtKB: Protein cereblon

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Macromolecule #2: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.097469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...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

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Macromolecule #3: Ras GTPase-activating protein-binding protein 2

MacromoleculeName: Ras GTPase-activating protein-binding protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.19807 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVMEKPSPLL VGREFVRQYY TLLNKAPEYL HRFYGRNSSY VHGGVDASGK PQEAVYGQND IHHKVLSLNF SECHTKIRHV DAHATLSDG VVVQVMGLLS NSGQPERKFM QTFVLAPEGS VPNKFYVHND MFRYEDEVFG DSEPELDEES EDEVEEEQEE R QPSPEPVQ ...String:
MVMEKPSPLL VGREFVRQYY TLLNKAPEYL HRFYGRNSSY VHGGVDASGK PQEAVYGQND IHHKVLSLNF SECHTKIRHV DAHATLSDG VVVQVMGLLS NSGQPERKFM QTFVLAPEGS VPNKFYVHND MFRYEDEVFG DSEPELDEES EDEVEEEQEE R QPSPEPVQ ENANSGYYEA HPVTNGIEEP LEESSHEPEP EPESETKTEE LKPQVEEKNL EELEEKSTTP PPAEPVSLPQ EP PKAFSWA SVTSKNLPPS GTVSSSGIPP HVKAPVSQPR VEAKPEVQSQ PPRVREQRPR ERPGFPPRGP RPGRGDMEQN DSD NRRIIR YPDSHQLFVG NLPHDIDENE LKEFFMSFGN VVELRINTKG VGGKLPNFGF VVFDDSEPVQ RILIAKPIMF RGEV RLNVE EKKTRAARER ETRGGGDDRR DIRRNDRGPG GPRGIVGGGM MRDRDGRGPP PRGGMAQKLG SGRGTGQMEG RFTGQ RR

UniProtKB: Ras GTPase-activating protein-binding protein 2

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo...

MacromoleculeName: (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1CED
Molecular weightTheoretical: 621.106 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.5056 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5fqd


Details: PDB ID 5DRV used as startup model for chains C and D
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 565661
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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