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- EMDB-49942: Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49942
TitleCryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24
Map data
Sample
  • Complex: CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24
    • Protein or peptide: Cyclin-dependent kinase 2
    • Protein or peptide: G1/S-specific cyclin-E1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
  • Ligand: N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide
  • Ligand: ZINC ION
Keywordskinase / degrader / CDK2 / Cyclin E / CELL CYCLE / CRBN
Function / homology
Function and homology information


positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / negative regulation of monoatomic ion transmembrane transport / RHOBTB3 ATPase cycle / 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 / cyclin-dependent protein serine/threonine kinase regulator activity / biological process involved in interaction with symbiont ...positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / negative regulation of monoatomic ion transmembrane transport / RHOBTB3 ATPase cycle / 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 / cyclin-dependent protein serine/threonine kinase regulator activity / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / regulation of heterochromatin organization / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / Cul4A-RING E3 ubiquitin ligase complex / X chromosome / Cul4-RING E3 ubiquitin ligase complex / G1/S-Specific Transcription / PTK6 Regulates Cell Cycle / Cul4B-RING E3 ubiquitin ligase complex / Association of TriC/CCT with target proteins during biosynthesis / regulation of anaphase-promoting complex-dependent catabolic process / ubiquitin ligase complex scaffold activity / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / negative regulation of reproductive process / negative regulation of developmental process / microtubule organizing center / locomotory exploration behavior / centrosome duplication / G0 and Early G1 / viral release from host cell / cullin family protein binding / DNA replication initiation / Telomere Extension By Telomerase / Activation of the pre-replicative complex / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of protein localization to chromatin / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / Activation of ATR in response to replication stress / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin E associated events during G1/S transition / Cajal body / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / proteasomal protein catabolic process / regulation of G2/M transition of mitotic cell cycle / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / positive regulation of gluconeogenesis / post-translational protein modification / regulation of mitotic cell cycle / telomere maintenance / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / nucleotide-excision repair / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / Recognition of DNA damage by PCNA-containing replication complex / peptidyl-serine phosphorylation / regulation of circadian rhythm / potassium ion transport / DNA Damage Recognition in GG-NER / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / G2/M transition of mitotic cell cycle / SCF(Skp2)-mediated degradation of p27/p21 / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Transcriptional regulation of granulopoiesis / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Orc1 removal from chromatin / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Lon N-terminal domain profile. / Lon protease, N-terminal domain ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / 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) / Cyclin, C-terminal domain / Cyclin_C / 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 / Cyclin, N-terminal / Cyclin, N-terminal domain / PUA-like superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / WD40-repeat-containing domain superfamily / 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
G1/S-specific cyclin-E1 / Cyclin-dependent kinase 2 / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCollier P / Zheng X / Ford M / Weiss M / Aversa R / Chen D / Li K / Growney JD / Yang A / Sathappa M ...Collier P / Zheng X / Ford M / Weiss M / Aversa R / Chen D / Li K / Growney JD / Yang A / Sathappa M / Breitkopf SB / Enerson B / Sawant R / Su L / Howarth L / Liang T / Paul A / Sharma K / Williams J / Kwiatkowski NP
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J Med Chem / Year: 2025
Title: Discovery of Selective and Orally Bioavailable Heterobifunctional Degraders of Cyclin-Dependent Kinase 2.
Authors: Philip N Collier / Xiaozhang Zheng / Melissa Ford / Matthew Weiss / Dapeng Chen / Kunhua Li / Joseph D Growney / Annan Yang / Murugappan Sathappa / Susanne B Breitkopf / Brad Enerson / Tong ...Authors: Philip N Collier / Xiaozhang Zheng / Melissa Ford / Matthew Weiss / Dapeng Chen / Kunhua Li / Joseph D Growney / Annan Yang / Murugappan Sathappa / Susanne B Breitkopf / Brad Enerson / Tong Liang / Atanu Paul / Rupa Sawant / Lijing Su / Robert J Aversa / Charles Howarth / Kirti Sharma / Juliet Williams / Nicholas P Kwiatkowski /
Abstract: Cyclin-dependent kinase 2 (CDK2) plays an important role in cell cycle regulation and has emerged as a compelling target for the treatment of cancer, largely because of its potential to overcome the ...Cyclin-dependent kinase 2 (CDK2) plays an important role in cell cycle regulation and has emerged as a compelling target for the treatment of cancer, largely because of its potential to overcome the resistance associated with CDK4/6 inhibition. Efforts to develop CDK2 inhibitors have historically proven challenging due to undesirable safety profiles associated with inhibiting off-target CDK isoforms. Herein, we describe the structure-guided discovery of a series of orally bioavailable and selective degraders of CDK2. Degrader demonstrated improved phenotypic selectivity compared to a clinical CDK2 inhibitor, with greater specificity for disease-relevant cyclin E1 (CCNE1)-amplified cancer cells vs nonamplified cohort. The antitumor activity of in mice bearing CCNE1-amplified HCC1569 tumors correlated with sustained >90% degradation of CDK2 and sustained 90% inhibition of Rb phosphorylation.
History
DepositionMar 28, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49942.png

Downloads & links

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Map

FileDownload / File: emd_49942.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.)
1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.0039170003 - 2.0743735
Average (Standard dev.)0.0009523255 (±0.022099247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49942_msk_1.map
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Additional map: #1

Fileemd_49942_additional_1.map
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Half map: #2

Fileemd_49942_half_map_1.map
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Half map: #1

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Sample components

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Entire : CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24

EntireName: CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24
Components
  • Complex: CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24
    • Protein or peptide: Cyclin-dependent kinase 2
    • Protein or peptide: G1/S-specific cyclin-E1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
  • Ligand: N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide
  • Ligand: ZINC ION

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Supramolecule #1: CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24

SupramoleculeName: CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cyclin-dependent kinase 2

MacromoleculeName: Cyclin-dependent kinase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.056469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPVRTY (TPO)HEVVTLWY ...String:
MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPVRTY (TPO)HEVVTLWY RAPEILLGCK YYSTAVDIWS LGCIFAEMVT RRALFPGDSE IDQLFRIFRT LGTPDEVVWP GVTSMPD YK PSFPKWARQD FSKVVPPLDE DGRSLLSQML HYDPNKRISA KAALAHPFFQ DVTKPVPHLR L

UniProtKB: Cyclin-dependent kinase 2

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Macromolecule #2: G1/S-specific cyclin-E1

MacromoleculeName: G1/S-specific cyclin-E1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.140578 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SGSIIAPSRG SPLPVLSWAN REEVWKIMLN KEKTYLRDQH FLEQHPLLQP KMRAILLDWL MEVCEVYKLH RETFYLAQDF FDRYMATQE NVVKTLLQLI GISSLFIAAK LEEIYPPKLH QFAYVTDGAC SGDEILTMEL MIMKALKWRL SPLTIVSWLN V YMQVAYLN ...String:
SGSIIAPSRG SPLPVLSWAN REEVWKIMLN KEKTYLRDQH FLEQHPLLQP KMRAILLDWL MEVCEVYKLH RETFYLAQDF FDRYMATQE NVVKTLLQLI GISSLFIAAK LEEIYPPKLH QFAYVTDGAC SGDEILTMEL MIMKALKWRL SPLTIVSWLN V YMQVAYLN DLHEVLLPQY PQQIFIQIAE LLDLCVLDVD CLEFPYGILA ASALYHFSSS ELMQKVSGYQ WCDIENCVKW MV PFAMVIR ETGSSKLKHF RGVADEDAHN IQTHRDSLDL LDKARAKKA

UniProtKB: G1/S-specific cyclin-E1

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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: 128.139578 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 TRIHWSHPQF EK

UniProtKB: DNA damage-binding protein 1

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Macromolecule #4: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.465375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSEAKKPNII NFDTSLPTSH TYLGADMEEF HGRTLHDDDS CQVIPVLPQV MMILIPGQTL PLQLFHPQEV SMVRNLIQKD RTFAVLAYS NVQEREAQFG TTAEIYAYRE EQDFGIEIVK VKAIGRQRFK VLELRTQSDG IQQAKVQILP ECVLPSTMSA V QLESLNKC ...String:
GSEAKKPNII NFDTSLPTSH TYLGADMEEF HGRTLHDDDS CQVIPVLPQV MMILIPGQTL PLQLFHPQEV SMVRNLIQKD RTFAVLAYS NVQEREAQFG TTAEIYAYRE EQDFGIEIVK VKAIGRQRFK VLELRTQSDG IQQAKVQILP ECVLPSTMSA V QLESLNKC QIFPSKPVSR EDQCSYKWWQ KYQKRKFHCA NLTSWPRWLY SLYDAETLMD RIKKQLREWD ENLKDDSLPS NP IDFSYRV AACLPIDDVL RIQLLKIGSA IQRLRCELDI MNKCTSLCCK QCQETEITTK NEIFSLSLCG PMAAYVNPHG YVH ETLTVY KACNLNLIGR PSTEHSWFPG YAWTVAQCKI CASHIGWKFT ATKKDMSPQK FWGLTRSALL PTIPDTEDEI SPDK VILCL

UniProtKB: Protein cereblon

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Macromolecule #5: N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropy...

MacromoleculeName: N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2- ...Name: N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1B7G
Molecular weightTheoretical: 845.373 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / 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: 7.5
Details: 50mM HEPES, pH 7.5, 150mM NaCl, 2mM TCEP, 2 mM FFC8, protein = 13.4 mg/ml
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

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Image processing

Particle selectionNumber selected: 576509
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 130033
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)
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
SoftwareName: PHENIX (ver. 1.20.1_4487:)
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9nyr:
Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24

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