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

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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 / negative regulation of monoatomic ion transmembrane transport / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair ...NEK6-subfamily protein kinase / negative regulation of monoatomic ion transmembrane transport / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / 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 / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of telomere maintenance / locomotory exploration behavior / microtubule organizing center / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / spindle assembly / EML4 and NUDC in mitotic spindle formation / positive regulation of gluconeogenesis / regulation of mitotic cell cycle / molecular function activator activity / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / 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 / positive regulation of protein catabolic process / Dual incision in TC-NER / spindle pole / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / eukaryotic translation initiation factor 2alpha kinase activity / chromosome, telomeric region / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / protein ubiquitination / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / apoptotic process / centrosome / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus
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) / RSE1/DDB1/CPSF1 second beta-propeller ...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. / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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: To Be Published
Title: Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7
Authors: Khoshouei M / Schroeder M
History
DepositionOct 22, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing 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
Contrast
Others
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

Projections

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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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Histogram

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Additional map: non-sharpened map

Fileemd_51881_additional_1.map
Annotationnon-sharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half A map

Fileemd_51881_half_map_1.map
Annotationhalf A map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map

Fileemd_51881_half_map_2.map
Annotationhalf B map
Projections & Slices
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Histogram

Histogram (log scale)

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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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