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- PDB-9w2f: Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR -

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Basic information

Entry
Database: PDB / ID: 9w2f
TitleCryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR
Components
  • DNA damage-binding protein 1
  • ELAV-like protein 1
  • Protein cereblon
KeywordsRNA BINDING PROTEIN / Molecular glue degrader / Complex
Function / homology
Function and homology information


positive regulation of autophagosome size / lncRNA-mediated post-transcriptional gene silencing / negative regulation of miRNA-mediated gene silencing / regulation of stem cell population maintenance / HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of monoatomic ion transmembrane transport / mRNA 3'-UTR AU-rich region binding / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei ...positive regulation of autophagosome size / lncRNA-mediated post-transcriptional gene silencing / negative regulation of miRNA-mediated gene silencing / regulation of stem cell population maintenance / HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of monoatomic ion transmembrane transport / mRNA 3'-UTR AU-rich region binding / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / miRNA binding / 3'-UTR-mediated mRNA stabilization / mRNA stabilization / UV-damage excision repair / biological process involved in interaction with symbiont / limb development / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / mRNA destabilization / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / lncRNA binding / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / sarcoplasm / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / response to glucose / positive regulation of Wnt signaling pathway / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / positive regulation of superoxide anion generation / proteasomal protein catabolic process / positive regulation of autophagy / positive regulation of gluconeogenesis / positive regulation of translation / nucleotide-excision repair / mRNA 3'-UTR binding / sperm end piece / P-body / 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 / Wnt signaling pathway / Formation of Incision Complex in GG-NER / cytoplasmic stress granule / protein import into nucleus / 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 / double-stranded RNA binding / site of double-strand break / sperm principal piece / Neddylation / cytoplasmic vesicle / sperm midpiece / Potential therapeutics for SARS / ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromosome, telomeric region / cell population proliferation / postsynapse / protein ubiquitination / ribonucleoprotein complex / DNA repair / mRNA binding / apoptotic process / DNA damage response / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / : / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / 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 ...HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / 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 / 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
: / ELAV-like protein 1 / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDou, H. / Zhu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Other private2024 China
Ministry of Education (MoE, China)JYB2025XDXM502 China
CitationJournal: To Be Published
Title: Molecular Glue Degraders of HuR Suppress BRAF-Mutant Colorectal Cancer
Authors: Dou, H.
History
DepositionJul 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Protein cereblon
C: ELAV-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8445
Polymers180,3643
Non-polymers4812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q16531
#2: Protein Protein cereblon


Mass: 43882.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q96SW2
#3: Protein ELAV-like protein 1 / Hu-antigen R / HuR


Mass: 9383.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELAVL1, HUR
Production host: Cloning vector pET-T7p(-3G)-lacO(SymR+1)-GFP-LVA (others)
References: UniProt: Q15717
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1EUN / (3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidine-2,6-dione


Mass: 415.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21N3O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of HuR-CRBN/DDB1 with dHuR-2 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Insect cell expression vector pTIE1 (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 484157 / Symmetry type: POINT

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