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Basic information

Entry
Database: EMDB / ID: EMD-69484
TitleCryo-EM structure of CDK2 in complex with CRBN/DDB1 and B11 local refinement (Masked on CDK2-CRBN-DDB1)
Map data
Sample
  • Complex: CDK2 in complex with CRBN/DDB1 and B11
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Cyclin-dependent kinase 2
    • Protein or peptide: DNA damage-binding protein 1
KeywordsCyclin-Dependent Kinase 2 / Cereblon / Molecular glue / Complex / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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
DepositionMar 2, 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_69484.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.31548488 - 0.65369934
Average (Standard dev.)-0.00030555058 (±0.013398608)
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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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: Cyclin-dependent kinase 2
    • Protein or peptide: DNA damage-binding protein 1

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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: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH GSDYKDDDDV DYDIPTTENL YFQGAMGSEA KKPNIINFDT SLPTSHTYLG ADMEEFHGRT LHDDDSCQVI PVLPQVMMIL IPGQTLPLQL FHPQEVSMVR NLIQKDRTFA VLAYSNVQER EAQFGTTAEI YAYREEQDFG IEIVKVKAIG RQRFKVLELR ...String:
MSYYHHHHHH GSDYKDDDDV DYDIPTTENL YFQGAMGSEA KKPNIINFDT SLPTSHTYLG ADMEEFHGRT LHDDDSCQVI PVLPQVMMIL IPGQTLPLQL FHPQEVSMVR NLIQKDRTFA VLAYSNVQER EAQFGTTAEI YAYREEQDFG IEIVKVKAIG RQRFKVLELR TQSDGIQQAK VQILPECVLP STMSAVQLES LNKCQIFPSK PVSREDQCSY KWWQKYQKRK FHCANLTSWP RWLYSLYDAE TLMDRIKKQL REWDENLKDD SLPSNPIDFS YRVAACLPID DVLRIQLLKI GSAIQRLRCE LDIMNKCTSL CCKQCQETEI TTKNEIFSLS LCGPMAAYVN PHGYVHETLT VYKACNLNLI GRPSTEHSWF PGYAWTVAQC KICASHIGWK FTATKKDMSP QKFWGLTRSA LLPTIPDTED EISPDKVILC LGSSGGGGSG GGSSGGGGSG GGGSSGVSGW RLFKKIS

UniProtKB: Protein cereblon

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Macromolecule #2: Cyclin-dependent kinase 2

MacromoleculeName: Cyclin-dependent kinase 2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DYDIGSPTTE NLYFQGAATM VFTLEDFVGD WEQTAAYNLD QVLEQGGVSS LLQNLAVSVT PIQRIVRSGE NALKIDIHVI IPYEGLSADQ MAQIEEVFKV VYPVDDHHFK VILPYGTLVI DGVTPNMLNY FGRPYEGIAV FDGKKITVTG TLWNGNKIID ...String:
MSYYHHHHHH DYDIGSPTTE NLYFQGAATM VFTLEDFVGD WEQTAAYNLD QVLEQGGVSS LLQNLAVSVT PIQRIVRSGE NALKIDIHVI IPYEGLSADQ MAQIEEVFKV VYPVDDHHFK VILPYGTLVI DGVTPNMLNY FGRPYEGIAV FDGKKITVTG TLWNGNKIID ERLITPDGSM LFRVTINSGS SGGGGSGGGG SSMENFQKVE KIGEGTYGVV YKARNKLTGE VVALKKIRLD TETEGVPSTA IREISLLKEL NHPNIVKLLD VIHTENKLYL VFEFLHQDLK KFMDASALTG IPLPLIKSYL FQLLQGLAFC HSHRVLHRDL KPQNLLINTE GAIKLADFGL ARAFGVPVRT YTHEVVTLWY RAPEILLGCK YYSTAVDIWS LGCIFAEMVT RRALFPGDSE IDQLFRIFRT LGTPDEVVWP GVTSMPDYKP SFPKWARQDF SKVVPPLDED GRSLLSQMLH YDPNKRISAK AALAHPFFQD VTKPVPHLRL ENLYFQGGGS GGSSVIKPEM KIKLRMEGAV NGHKFVIEGE GIGKPYEGTQ TLDLTVEEGA PLPFSYDILT PAFQYGNRAF TKYPEDIPDY FKQAFPEGYS WERSMTYEDQ GICIATSDIT MEGDCFFYEI RFDGTNFPPN GPVMQKKTLK WEPSTEKMYV EDGVLKGDVE MALLLEGGGH YRCDFKTTYK AKKDVRLPDA HEVDHRIEIL SHDKDYNKVR LYEHAEARY

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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL RVELLGETSI AECLTYLDNG VVFVGSRLGD SQLVKLNVDS NEQGSYVVAM ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGGNGNS GEIQKLHIRT VPLYESPRKI CYQEVSQCFG VLSSRIEVQD TSGGTTALRP SASTQALSSS VSSSKLFSSS TAPHETSFGE EVEVHNLLII DQHTFEVLHA HQFLQNEYAL SLVSCKLGKD PNTYFIVGTA MVYPEEAEPK QGRIVVFQYS DGKLQTVAEK EVKGAVYSMV EFNGKLLASI NSTVRLYEWT TEKELRTECN HYNNIMALYL KTKGDFILVG DLMRSVLLLA YKPMEGNFEE IARDFNPNWM SAVEILDDDN FLGAENAFNL FVCQKDSAAT TDEERQHLQE VGLFHLGEFV NVFCHGSLVM QNLGETSTPT QGSVLFGTVN GMIGLVTSLS ESWYNLLLDM QNRLNKVIKS VGKIEHSFWR SFHTERKTEP ATGFIDGDLI ESFLDISRPK MQEVVANLQY DDGSGMKREA TADDLIKVVE ELTRIH

UniProtKB: DNA damage-binding protein 1

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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: 2.7 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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Atomic model buiding 1

Initial modelPDB ID:

9d0w


Chain - Source name: PDB / Chain - Initial model type: experimental model

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