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- EMDB-42247: Degrader-induced complex between PTPN2 and CRBN-DDB1 -

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Entry
Database: EMDB / ID: EMD-42247
TitleDegrader-induced complex between PTPN2 and CRBN-DDB1
Map data
Sample
  • Complex: CRBN-DDB1-PTPN2 complex
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Tyrosine-protein phosphatase non-receptor type 2
  • Ligand: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid
  • Ligand: ZINC ION
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of interleukin-2-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / negative regulation of positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / negative regulation of macrophage differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of chemotaxis ...negative regulation of interleukin-2-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / negative regulation of positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / negative regulation of macrophage differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of chemotaxis / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of monoatomic ion transmembrane transport / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / Interleukin-37 signaling / biological process involved in interaction with symbiont / syntaxin binding / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon-mediated signaling pathway / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of T cell receptor signaling pathway / STAT family protein binding / regulation of hepatocyte growth factor receptor signaling pathway / insulin receptor recycling / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of type II interferon-mediated signaling pathway / locomotory exploration behavior / cullin family protein binding / viral release from host cell / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of lipid storage / T cell differentiation / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / positive regulation of Wnt signaling pathway / negative regulation of tumor necrosis factor-mediated signaling pathway / ectopic germ cell programmed cell death / proteasomal protein catabolic process / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / Regulation of IFNG signaling / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / B cell differentiation / protein-tyrosine-phosphatase / erythrocyte differentiation / protein tyrosine phosphatase activity / endosome lumen / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / positive regulation of protein-containing complex assembly / PKR-mediated signaling / regulation of circadian rhythm / Negative regulation of MET activity / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / 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 / integrin binding / rhythmic process / insulin receptor signaling pathway / glucose homeostasis / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / Potential therapeutics for SARS / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / negative regulation of cell population proliferation / DNA repair / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / apoptotic process / protein kinase binding / perinuclear region of cytoplasm
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Cleavage/polyadenylation specificity factor, A subunit, N-terminal ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / CPSF A subunit region / Protein-tyrosine phosphatase, non-receptor type-1/2 / : / PUA-like superfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 2 / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCatalano C / Bratkowski M / Scapin G / Hao Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2024
Title: Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex.
Authors: Qi Hao / Manoj K Rathinaswamy / Kelly L Klinge / Matthew Bratkowski / Amirhossein Mafi / Christina K Baumgartner / Keith M Hamel / Gesine K Veits / Rinku Jain / Claudio Catalano / Mark ...Authors: Qi Hao / Manoj K Rathinaswamy / Kelly L Klinge / Matthew Bratkowski / Amirhossein Mafi / Christina K Baumgartner / Keith M Hamel / Gesine K Veits / Rinku Jain / Claudio Catalano / Mark Fitzgerald / Alexander W Hird / Eunice Park / Harit U Vora / James A Henderson / Kenton Longenecker / Charles W Hutchins / Wei Qiu / Giovanna Scapin / Qi Sun / Vincent S Stoll / Chaohong Sun / Ping Li / Dan Eaton / David Stokoe / Stewart L Fisher / Christopher G Nasveschuk / Marcia Paddock / Michael E Kort /
Abstract: PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in ...PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4, and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.
History
DepositionOct 6, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42247.png

Downloads & links

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Map

FileDownload / File: emd_42247.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.23383439 - 0.53737986
Average (Standard dev.)0.000052379906 (±0.015105324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42247_msk_1.map
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Half map: #2

Fileemd_42247_half_map_1.map
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Half map: #1

Fileemd_42247_half_map_2.map
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Sample components

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Entire : CRBN-DDB1-PTPN2 complex

EntireName: CRBN-DDB1-PTPN2 complex
Components
  • Complex: CRBN-DDB1-PTPN2 complex
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Tyrosine-protein phosphatase non-receptor type 2
  • Ligand: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid
  • Ligand: ZINC ION

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Supramolecule #1: CRBN-DDB1-PTPN2 complex

SupramoleculeName: CRBN-DDB1-PTPN2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 217.81996 KDa

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 128.33382 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGKI AVMELFRPKG ESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK E LKAFNIRL ...String:
MHHHHHHHHM SYNYVVTAQK PTAVNGCVTG HFTSAEDLNL LIAKNTRLEI YVVTAEGLRP VKEVGMYGKI AVMELFRPKG ESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK E LKAFNIRL EELHVIDVKF LYGCQAPTIC FVYQDPQGRH VKTYEVSLRE KEFNKGPWKQ ENVEAEASMV IAVPEPFGGA II IGQESIT YHNGDKYLAI APPIIKQSTI VCHNRVDPNG SRYLLGDMEG RLFMLLLEKE EQMDGTVTLK DLRVELLGET SIA ECLTYL DNGVVFVGSR LGDSQLVKLN VDSNEQGSYV VAMETFTNLG PIVDMCVVDL ERQGQGQLVT CSGAFKEGSL RIIR NGIGI HEHASIDLPG IKGLWPLRSD PNRETDDTLV LSFVGQTRVL MLNGEEVEET ELMGFVDDQQ TFFCGNVAHQ QLIQI TSAS VRLVSQEPKA LVSEWKEPQA KNISVASCNS SQVVVAVGRA LYYLQIHPQE LRQISHTEME HEVACLDITP LGDSNG LSP LCAIGLWTDI SARILKLPSF ELLHKEMLGG EIIPRSILMT TFESSHYLLC ALGDGALFYF GLNIETGLLS DRKKVTL GT QPTVLRTFRS LSTTNVFACS DRPTVIYSSN HKLVFSNVNL KEVNYMCPLN SDGYPDSLAL ANNSTLTIGT IDEIQKLH I RTVPLYESPR KICYQEVSQC FGVLSSRIEV QDTSGGTTAL RPSASTQALS SSVSSSKLFS SSTAPHETSF GEEVEVHNL LIIDQHTFEV LHAHQFLQNE YALSLVSCKL GKDPNTYFIV GTAMVYPEEA EPKQGRIVVF QYSDGKLQTV AEKEVKGAVY SMVEFNGKL LASINSTVRL YEWTTEKELR TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN P NWMSAVEI LDDDNFLGAE NAFNLFVCQK DSAATTDEER QHLQEVGLFH LGEFVNVFCH GSLVMQNLGE TSTPTQGSVL FG TVNGMIG LVTSLSESWY NLLLDMQNRL NKVIKSVGKI EHSFWRSFHT ERKTEPATGF IDGDLIESFL DISRPKMQEV VAN LQYDDG SGMKREATAD DLIKVVEELT RIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.77702 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKM AGEGDQQDAA HNMGNHLPLL PAESEEEDEM EVEDQDSKEA KKPNIINFDT SLPTSHTYLG ADMEEFHGRT LHDDDSCQV IPVLPQVMMI LIPGQTLPLQ LFHPQEVSMV RNLIQKDRTF AVLAYSNVQE REAQFGTTAE IYAYREEQDF G IEIVKVKA ...String:
MWSHPQFEKM AGEGDQQDAA HNMGNHLPLL PAESEEEDEM EVEDQDSKEA KKPNIINFDT SLPTSHTYLG ADMEEFHGRT LHDDDSCQV IPVLPQVMMI LIPGQTLPLQ LFHPQEVSMV RNLIQKDRTF AVLAYSNVQE REAQFGTTAE IYAYREEQDF G IEIVKVKA IGRQRFKVLE LRTQSDGIQQ AKVQILPECV LPSTMSAVQL ESLNKCQIFP SKPVSREDQC SYKWWQKYQK RK FHCANLT SWPRWLYSLY DAETLMDRIK KQLREWDENL KDDSLPSNPI DFSYRVAACL PIDDVLRIQL LKIGSAIQRL RCE LDIMNK CTSLCCKQCQ ETEITTKNEI FSLSLCGPMA AYVNPHGYVH ETLTVYKACN LNLIGRPSTE HSWFPGYAWT VAQC KICAS HIGWKFTATK KDMSPQKFWG LTRSALLPTI PDTEDEISPD KVILCL

UniProtKB: Protein cereblon

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Macromolecule #3: Tyrosine-protein phosphatase non-receptor type 2

MacromoleculeName: Tyrosine-protein phosphatase non-receptor type 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-tyrosine-phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.966 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMPTTIERE FEELDTQRRW QPLYLEIRNE SHDYPHRVAK FPENRNRNRY RDVSPYDHSR VKLQNAENDY INASLVDIEE AQRSYILTQ GPLPNTCCHF WLMVWQQKTK AVVMLNRIVE KESVKCAQYW PTDDQEMLFK ETGFSVKLLS EDVKSYYTVH L LQLENINS ...String:
MAMPTTIERE FEELDTQRRW QPLYLEIRNE SHDYPHRVAK FPENRNRNRY RDVSPYDHSR VKLQNAENDY INASLVDIEE AQRSYILTQ GPLPNTCCHF WLMVWQQKTK AVVMLNRIVE KESVKCAQYW PTDDQEMLFK ETGFSVKLLS EDVKSYYTVH L LQLENINS GETRTISHFH YTTWPDFGVP ESPASFLNFL FKVRESGSLN PDHGPAVIHC SAGIGRSGTF SLVDTCLVLM EK GDDINIK QVLLNMRKYR MGLIQTPDQL RFSYMAIIEG AKCIKGDSSI QKRWKELSKE DLSPAFDHSP NKIMTEKYNH HHH HHHH

UniProtKB: Tyrosine-protein phosphatase non-receptor type 2

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Macromolecule #4: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2...

MacromoleculeName: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2- ...Name: (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid
type: ligand / ID: 4 / Number of copies: 1 / Formula: WO8
Molecular weightTheoretical: 976.512 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.09 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69542
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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