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- PDB-9q33: Cereblon Ternary Complex with Blimp1 and compound 5 -

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Basic information

Entry
Database: PDB / ID: 9q33
TitleCereblon Ternary Complex with Blimp1 and compound 5
Components
  • PR domain zinc finger protein 1
  • Protein cereblon
KeywordsLIGASE / Liganded Cereblon Ligase Substrate
Function / homology
Function and homology information


regulation of extrathymic T cell differentiation / regulation of NK T cell differentiation / sebum secreting cell proliferation / morphogenesis of a branching structure / retinal bipolar neuron differentiation / regulation of natural killer cell differentiation / maternal placenta development / Specification of primordial germ cells / trophoblast giant cell differentiation / eye photoreceptor cell development ...regulation of extrathymic T cell differentiation / regulation of NK T cell differentiation / sebum secreting cell proliferation / morphogenesis of a branching structure / retinal bipolar neuron differentiation / regulation of natural killer cell differentiation / maternal placenta development / Specification of primordial germ cells / trophoblast giant cell differentiation / eye photoreceptor cell development / negative regulation of monoatomic ion transmembrane transport / histone methyltransferase binding / intestinal epithelial cell development / heart valve development / coronary vasculature development / STAT3 nuclear events downstream of ALK signaling / Regulation of TP53 Expression / artery morphogenesis / aorta development / ventricular septum development / Cul4A-RING E3 ubiquitin ligase complex / germ cell development / locomotory exploration behavior / cell fate commitment / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / methyltransferase activity / promoter-specific chromatin binding / kidney development / positive regulation of protein-containing complex assembly / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / methylation / gene expression / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / adaptive immune response / transmembrane transporter binding / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
PR domain zinc finger protein 1 / PRDM1, PR/SET domain / PR domain zinc finger protein 2, PR 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 ...PR domain zinc finger protein 1 / PRDM1, PR/SET domain / PR domain zinc finger protein 2, PR 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) / PUA-like superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain profile. / SET domain superfamily / SET domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
: / PR domain zinc finger protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWatson, E.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J Med Chem / Year: 2025
Title: Discovery and Characterization of Novel BLIMP-1 Heterobifunctional Ligand-Directed Degraders.
Authors: Bryan J Simmons / Lynda Groocock / Jesus Moreno / David S Peters / Meredith E Hughes / Vijay Veeravalli / Jennifer M Crawford / Matthew Chalkley / Mark Griffith / Melissa Plooster / Bo Hu / ...Authors: Bryan J Simmons / Lynda Groocock / Jesus Moreno / David S Peters / Meredith E Hughes / Vijay Veeravalli / Jennifer M Crawford / Matthew Chalkley / Mark Griffith / Melissa Plooster / Bo Hu / Jim Gamez / Jim Leisten / Michael J Barnes / Jason Chinn / Gauri Deb / Hardik Modi / Madhu Katepalli / Dahlia Weiss / Walter Won / Zhenghang Sun / Shan Yu / Cameron Reid / Andrew F Donnell / Ling Li / Edmond R Watson / Sophie Perrin-Ninkovic / Lihong Shi / Rama Krishna Narla / Christoph W Zapf / Neil Bence / Antonia Lopez-Girona / Jennifer R Riggs /
Abstract: B-lymphocyte-induced maturation protein 1 (BLIMP-1/PRDM1) is a master transcriptional repressor essential for terminal differentiation of activated B-cells into bone-marrow resident plasma cells. ...B-lymphocyte-induced maturation protein 1 (BLIMP-1/PRDM1) is a master transcriptional repressor essential for terminal differentiation of activated B-cells into bone-marrow resident plasma cells. Multiple myeloma (MM) is a plasma cell malignancy wherein the BLIMP-1 regulon remains critical to support basal cell functions, such as an elevated metabolic state and immunoglobulin production that underlie disease manifestation and tumor cell proliferation. It is predicted that perturbation of BLIMP-1 will significantly impact tumor cell homeostasis and ultimately reduce MM cell survival. Herein, we describe the discovery and optimization of the first orally bioavailable BLIMP-1 heterobifunctional ligand-directed degrader (LDD) and demonstration of the expected antitumor response and immunomodulatory biology following BLIMP-1 degradation using preclinical in vivo MM models.
History
DepositionAug 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR domain zinc finger protein 1
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3114
Polymers72,4692
Non-polymers8422
Water00
1
A: PR domain zinc finger protein 1


Theoretical massNumber of molelcules
Total (without water)21,8661
Polymers21,8661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4463
Polymers50,6041
Non-polymers8422
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein PR domain zinc finger protein 1 / BLIMP-1 / Beta-interferon gene positive regulatory domain I-binding factor / PR domain-containing ...BLIMP-1 / Beta-interferon gene positive regulatory domain I-binding factor / PR domain-containing protein 1 / Positive regulatory domain I-binding factor 1 / PRDI-BF1 / PRDI-binding factor 1


Mass: 21865.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 37-222 / Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM1, BLIMP1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O75626, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Protein cereblon


Mass: 50603.676 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1CN1 / N-({(4R)-7-[(1S)-2-amino-1-(4-bromo-2-methylphenyl)-2-oxoethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyrazin-3-yl}methyl)-13-{4-[(3R)-2,6-dioxopiperidin-3-yl]anilino}tridecanamide


Mass: 776.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54BrN7O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Cereblon Ternary Complex with Blimp1 and compound 5 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174443 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044511
ELECTRON MICROSCOPYf_angle_d0.6356118
ELECTRON MICROSCOPYf_dihedral_angle_d10.143647
ELECTRON MICROSCOPYf_chiral_restr0.044654
ELECTRON MICROSCOPYf_plane_restr0.006785

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