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- EMDB-51881: Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 -

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Basic information

Entry
Database: EMDB / ID: EMD-51881
TitleCryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7
Map datasharpened map
Sample
  • Complex: Ternary complex of hDDB1-hCRBN with NK7-902 and hNEK7
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Serine/threonine-protein kinase Nek7
    • Protein or peptide: Protein cereblon
  • Ligand: 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione
KeywordsCRBN / DDB1 / NEK7 / TRANSFERASE
Function / homology
Function and homology information


NEK6-subfamily protein kinase / regulation of kinase activity / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / negative regulation of monoatomic ion transmembrane transport / cellular response to potassium ion / 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 ...NEK6-subfamily protein kinase / regulation of kinase activity / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / negative regulation of monoatomic ion transmembrane transport / cellular response to potassium ion / 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 cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / locomotory exploration behavior / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of NLRP3 inflammasome complex assembly / microtubule organizing center / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / positive regulation of telomere maintenance / regulation of cellular response to stress / limb development / viral release from host cell / cullin family protein binding / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / positive regulation of gluconeogenesis / spindle assembly / EML4 and NUDC in mitotic spindle formation / regulation of embryonic development / replication fork processing / molecular function activator activity / regulation of mitotic cell cycle / proteasomal protein catabolic process / epigenetic regulation of gene expression / positive regulation of protein-containing complex assembly / nucleotide-excision repair / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / cell population proliferation / 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 / spindle pole / Formation of Incision Complex in GG-NER / positive regulation of protein catabolic process / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / rhythmic process / regulation of cell population proliferation / site of double-strand break / Neddylation / spermatogenesis / ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / regulation of apoptotic process / transmembrane transporter binding / protein-macromolecule adaptor activity / protein phosphorylation / chromosome, telomeric region / protein ubiquitination / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA damage response / nucleolus / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / DNA binding / : / extracellular exosome / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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) / : ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / Serine/threonine-protein kinase Nek7 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKhoshouei M / Schroeder M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2024
Title: A cereblon (CRBN) molecular glue degrader of NIMA-related kinase 7 (NEK7) reveals a context-dependent role in NLRP3 inflammasome activation
Authors: Sylvain A / Stoehr N / Ma F / Cernijenko A / Schroder M / Khoshouei M / Vogelsanger M / Schoenboerner M / Burke A / Pasupuleti R / Solomon J / Paulk J / Xu L / Dawson J / Begue D / Lefeuvre ...Authors: Sylvain A / Stoehr N / Ma F / Cernijenko A / Schroder M / Khoshouei M / Vogelsanger M / Schoenboerner M / Burke A / Pasupuleti R / Solomon J / Paulk J / Xu L / Dawson J / Begue D / Lefeuvre P / Ahrne E / Hofmann A / Dickson CJ / Arabin P / Zimmerlin A / Kiffe M / Froehlicher M / Boersig T / Elhajouji A / Brichet M / Menon S / Liu S / Mueller M / Wartchow C / Lin J / Cardona Gloria Y / Dickhofer S / Weber ANR / Welzel T / Kuemmerle-Deschner J / Farady CJ / Pulz R / Bornancin F / Buckley DL / Bassi ZI
History
DepositionOct 22, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51881.png

Downloads & links

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Map

FileDownload / File: emd_51881.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 340 pix.
= 287.3 Å		0.85 Å/pix.
x 340 pix.
= 287.3 Å		0.85 Å/pix.
x 340 pix.
= 287.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.2196026 - 2.1957734
Average (Standard dev.)-0.0004020574 (±0.034498736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 287.30002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51881_msk_1.map
Projections & Slices
AxesZYX

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Additional map: non-sharpened map

Fileemd_51881_additional_1.map
Annotationnon-sharpened map
Projections & Slices
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Half map: half A map

Fileemd_51881_half_map_1.map
Annotationhalf A map
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Half map: half B map

Fileemd_51881_half_map_2.map
Annotationhalf B map
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Sample components

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Entire : Ternary complex of hDDB1-hCRBN with NK7-902 and hNEK7

EntireName: Ternary complex of hDDB1-hCRBN with NK7-902 and hNEK7
Components
  • Complex: Ternary complex of hDDB1-hCRBN with NK7-902 and hNEK7
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Serine/threonine-protein kinase Nek7
    • Protein or peptide: Protein cereblon
  • Ligand: 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione

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Supramolecule #1: Ternary complex of hDDB1-hCRBN with NK7-902 and hNEK7

SupramoleculeName: Ternary complex of hDDB1-hCRBN with NK7-902 and hNEK7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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: 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 #2: Serine/threonine-protein kinase Nek7

MacromoleculeName: Serine/threonine-protein kinase Nek7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NEK6-subfamily protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.753137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMDEQSQGM QGPPVPQFQP QKALRPDMGY NTLANFRIEK KIGRGQFSEV YRAACLLDGV PVALKKVQIF DLMDAKARAD CIKEIDLLK QLNHPNVIKY YASFIEDNEL NIVLELADAG DLSRMIKHFK KQKRLIPERT VWKYFVQLCS ALEHMHSRRV M HRDIKPAN ...String:
GPMDEQSQGM QGPPVPQFQP QKALRPDMGY NTLANFRIEK KIGRGQFSEV YRAACLLDGV PVALKKVQIF DLMDAKARAD CIKEIDLLK QLNHPNVIKY YASFIEDNEL NIVLELADAG DLSRMIKHFK KQKRLIPERT VWKYFVQLCS ALEHMHSRRV M HRDIKPAN VFITATGVVK LGDLGLGRFF SSKTTAAHSL VGTPYYMSPE RIHENGYNFK SDIWSLGCLL YEMAALQSPF YG DKMNLYS LCKKIEQCDY PPLPSDHYSE ELRQLVNMCI NPDPEKRPDV TYVYDVAKRM HACTASS

UniProtKB: Serine/threonine-protein kinase Nek7

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Macromolecule #3: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.517762 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGGSHHHHHH LEVLFQGPAG EGDQQDAAHN MGNHLPLLPA ESEEEDEMEV EDQDSKEAKK PNIINFDTSL PTSHTYLGAD MEEFHGRTL HDDDSCQVIP VLPQVMMILI PGQTLPLQLF HPQEVSMVRN LIQKDRTFAV LAYSNVQERE AQFGTTAEIY A YREEQDFG ...String:
MGGSHHHHHH LEVLFQGPAG EGDQQDAAHN MGNHLPLLPA ESEEEDEMEV EDQDSKEAKK PNIINFDTSL PTSHTYLGAD MEEFHGRTL HDDDSCQVIP VLPQVMMILI PGQTLPLQLF HPQEVSMVRN LIQKDRTFAV LAYSNVQERE AQFGTTAEIY A YREEQDFG IEIVKVKAIG RQRFKVLELR TQSDGIQQAK VQILPECVLP STMSAVQLES LNKCQIFPSK PVSREDQCSY KW WQKYQKR KFHCANLTSW PRWLYSLYDA ETLMDRIKKQ LREWDENLKD DSLPSNPIDF SYRVAACLPI DDVLRIQLLK IGS AIQRLR CELDIMNKCT SLCCKQCQET EITTKNEIFS LSLCGPMAAY VNPHGYVHET LTVYKACNLN LIGRPSTEHS WFPG YAWTV AQCKICASHI GWKFTATKKD MSPQKFWGLT RSALLPTIPD TEDEISPDKV ILCL

UniProtKB: Protein cereblon

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Macromolecule #4: 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(et...

MacromoleculeName: 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1ISP
Molecular weightTheoretical: 410.466 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 16.09 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm

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Image processing

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

5fqd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 327074
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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