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Basic information

Entry
Database: EMDB / ID: EMD-69221
TitleCryo-EM structure of CDK2 in complex with CRBN/DDB1 and B11
Map data
Sample
  • Complex: CDK2 in complex with CRBN/DDB1 and B11
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Oplophorus-luciferin 2-monooxygenase catalytic subunit,Cyclin-dependent kinase 2,GFP-like fluorescent chromoprotein
    • Protein or peptide: DNA damage-binding protein 1
  • Ligand: spiro[3.3]heptan-2-ylmethyl ~{N}-[[3-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]-8-chloranyl-6-fluoranyl-4-oxidanylidene-quinazolin-7-yl]methyl]carbamate
KeywordsCyclin-Dependent Kinase 2 / Cereblon / Molecular glue / Complex / CELL CYCLE
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsLi XZ / Jiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2026
Title: Selective CDK2 Degradation via Noncanonical Recruitment.
Authors: Pei Y / Lin W / Li X / Meng Y / Yin Y / Pan B / Zhou L / Cao L / Cang Y / Jiang Y / Lu W / Meng Z
History
DepositionFeb 16, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69221.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.25313783 - 0.84744674
Average (Standard dev.)0.0013693046 (±0.013918459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69221_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_69221_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CDK2 in complex with CRBN/DDB1 and B11

EntireName: CDK2 in complex with CRBN/DDB1 and B11
Components
  • Complex: CDK2 in complex with CRBN/DDB1 and B11
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Oplophorus-luciferin 2-monooxygenase catalytic subunit,Cyclin-dependent kinase 2,GFP-like fluorescent chromoprotein
    • Protein or peptide: DNA damage-binding protein 1
  • Ligand: spiro[3.3]heptan-2-ylmethyl ~{N}-[[3-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]-8-chloranyl-6-fluoranyl-4-oxidanylidene-quinazolin-7-yl]methyl]carbamate

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Supramolecule #1: CDK2 in complex with CRBN/DDB1 and B11

SupramoleculeName: CDK2 in complex with CRBN/DDB1 and B11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.781996 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH GSDYKDDDDV DYDIPTTENL YFQGAMGSEA KKPNIINFDT SLPTSHTYLG ADMEEFHGRT LHDDDSCQVI PVLPQVMMI LIPGQTLPLQ LFHPQEVSMV RNLIQKDRTF AVLAYSNVQE REAQFGTTAE IYAYREEQDF GIEIVKVKAI G RQRFKVLE ...String:
MSYYHHHHHH GSDYKDDDDV DYDIPTTENL YFQGAMGSEA KKPNIINFDT SLPTSHTYLG ADMEEFHGRT LHDDDSCQVI PVLPQVMMI LIPGQTLPLQ LFHPQEVSMV RNLIQKDRTF AVLAYSNVQE REAQFGTTAE IYAYREEQDF GIEIVKVKAI G RQRFKVLE LRTQSDGIQQ AKVQILPECV LPSTMSAVQL ESLNKCQIFP SKPVSREDQC SYKWWQKYQK RKFHCANLTS WP RWLYSLY DAETLMDRIK KQLREWDENL KDDSLPSNPI DFSYRVAACL PIDDVLRIQL LKIGSAIQRL RCELDIMNKC TSL CCKQCQ ETEITTKNEI FSLSLCGPMA AYVNPHGYVH ETLTVYKACN LNLIGRPSTE HSWFPGYAWT VAQCKICASH IGWK FTATK KDMSPQKFWG LTRSALLPTI PDTEDEISPD KVILCLGSSG GGGSGGGSSG GGGSGGGGSS GVSGWRLFKK IS

UniProtKB: Protein cereblon

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Macromolecule #2: Oplophorus-luciferin 2-monooxygenase catalytic subunit,Cyclin-dep...

MacromoleculeName: Oplophorus-luciferin 2-monooxygenase catalytic subunit,Cyclin-dependent kinase 2,GFP-like fluorescent chromoprotein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 82.203477 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DYDIGSPTTE NLYFQGAATM VFTLEDFVGD WEQTAAYNLD QVLEQGGVSS LLQNLAVSVT PIQRIVRSGE NALKIDIHV IIPYEGLSAD QMAQIEEVFK VVYPVDDHHF KVILPYGTLV IDGVTPNMLN YFGRPYEGIA VFDGKKITVT G TLWNGNKI ...String:
MSYYHHHHHH DYDIGSPTTE NLYFQGAATM VFTLEDFVGD WEQTAAYNLD QVLEQGGVSS LLQNLAVSVT PIQRIVRSGE NALKIDIHV IIPYEGLSAD QMAQIEEVFK VVYPVDDHHF KVILPYGTLV IDGVTPNMLN YFGRPYEGIA VFDGKKITVT G TLWNGNKI IDERLITPDG SMLFRVTINS GSSGGGGSGG GGSSMENFQK VEKIGEGTYG VVYKARNKLT GEVVALKKIR LD TETEGVP STAIREISLL KELNHPNIVK LLDVIHTENK LYLVFEFLHQ DLKKFMDASA LTGIPLPLIK SYLFQLLQGL AFC HSHRVL HRDLKPQNLL INTEGAIKLA DFGLARAFGV PVRTYTHEVV TLWYRAPEIL LGCKYYSTAV DIWSLGCIFA EMVT RRALF PGDSEIDQLF RIFRTLGTPD EVVWPGVTSM PDYKPSFPKW ARQDFSKVVP PLDEDGRSLL SQMLHYDPNK RISAK AALA HPFFQDVTKP VPHLRLENLY FQGGGSGGSS VIKPEMKIKL RMEGAVNGHK FVIEGEGIGK PYEGTQTLDL TVEEGA PLP FSYDILTPAF QYGNRAFTKY PEDIPDYFKQ AFPEGYSWER SMTYEDQGIC IATSDITMEG DCFFYEIRFD GTNFPPN GP VMQKKTLKWE PSTEKMYVED GVLKGDVEMA LLLEGGGHYR CDFKTTYKAK KDVRLPDAHE VDHRIEILSH DKDYNKVR L YEHAEARY

UniProtKB: Cyclin-dependent kinase 2

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Macromolecule #3: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.347078 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 LRIIRNGIGG NGNS GEIQK LHIRTVPLYE SPRKICYQEV SQCFGVLSSR IEVQDTSGGT TALRPSASTQ ALSSSVSSSK LFSSSTAPHE TSFGE EVEV HNLLIIDQHT FEVLHAHQFL QNEYALSLVS CKLGKDPNTY FIVGTAMVYP EEAEPKQGRI VVFQYSDGKL QTVAEK EVK GAVYSMVEFN GKLLASINST VRLYEWTTEK ELRTECNHYN NIMALYLKTK GDFILVGDLM RSVLLLAYKP MEGNFEE IA RDFNPNWMSA VEILDDDNFL GAENAFNLFV CQKDSAATTD EERQHLQEVG LFHLGEFVNV FCHGSLVMQN LGETSTPT Q GSVLFGTVNG MIGLVTSLSE SWYNLLLDMQ NRLNKVIKSV GKIEHSFWRS FHTERKTEPA TGFIDGDLIE SFLDISRPK MQEVVANLQY DDGSGMKREA TADDLIKVVE ELTRIH

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Macromolecule #4: spiro[3.3]heptan-2-ylmethyl ~{N}-[[3-[(3~{R})-2,6-bis(oxidanylide...

MacromoleculeName: spiro[3.3]heptan-2-ylmethyl ~{N}-[[3-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]-8-chloranyl-6-fluoranyl-4-oxidanylidene-quinazolin-7-yl]methyl]carbamate
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1E59
Molecular weightTheoretical: 490.912 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

Concentration14 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 498215
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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