+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19408 | |||||||||
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Title | Cryo-EM structure of CDK2-cyclin A in complex with CDC25A | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cell-cycle / CDK / phosphatase / cancer / CELL CYCLE | |||||||||
Function / homology | Function and homology information positive regulation of G2/MI transition of meiotic cell cycle / cell cycle G1/S phase transition / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex ...positive regulation of G2/MI transition of meiotic cell cycle / cell cycle G1/S phase transition / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / 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 / X chromosome / PTK6 Regulates Cell Cycle / regulation of DNA replication / regulation of anaphase-promoting complex-dependent catabolic process / 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 / phosphoprotein phosphatase activity / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / cellular response to nitric oxide / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / : / cyclin binding / protein-tyrosine-phosphatase / post-translational protein modification / positive regulation of DNA replication / meiotic cell cycle / protein tyrosine phosphatase activity / male germ cell nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / response to radiation / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular response to UV / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / protein-folding chaperone binding / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / cell population proliferation / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Rowland RJ / Noble MEM / Endicott JA | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the CDK2-cyclin A-CDC25A Complex Authors: Rowland RJ / Korolchuk S / Salamina M / Ault JR / Hart S / Turkenburg JP / Blaza JN / Noble MEM / Endicott JA | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19408.map.gz | 85.8 MB | EMDB map data format | |
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Header (meta data) | emd-19408-v30.xml emd-19408.xml | 21 KB 21 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19408_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_19408.png | 122.1 KB | ||
Masks | emd_19408_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-19408.cif.gz | 6.9 KB | ||
Others | emd_19408_half_map_1.map.gz emd_19408_half_map_2.map.gz | 84.6 MB 84.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19408 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19408 | HTTPS FTP |
-Related structure data
Related structure data | 8rozMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19408.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19408_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19408_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19408_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trimeric complex of CDK2-cyclin A-CDC25A
Entire | Name: Trimeric complex of CDK2-cyclin A-CDC25A |
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Components |
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-Supramolecule #1: Trimeric complex of CDK2-cyclin A-CDC25A
Supramolecule | Name: Trimeric complex of CDK2-cyclin A-CDC25A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 86 KDa |
-Macromolecule #1: Cyclin-dependent kinase 2
Macromolecule | Name: Cyclin-dependent kinase 2 / type: protein_or_peptide / ID: 1 Details: Human cyclin dependant protein kinase 2 (CDK2) phosphorylated at Tyr15 and Thr160 Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.136449 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MENFQKVEKI GEGT(PTR)GVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKL YLV FEFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPV RT Y(TPO) ...String: MENFQKVEKI GEGT(PTR)GVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKL YLV FEFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPV RT Y(TPO)HEVVTLWY RAPEILLGCK YYSTAVDIWS LGCIFAEMVT RRALFPGDSE IDQLFRIFRT LGTPDEVVWP GVTS MPDYK PSFPKWARQD FSKVVPPLDE DGRSLLSQML HYDPNKRISA KAALAHPFFQ DVTKPVPHLR L UniProtKB: Cyclin-dependent kinase 2 |
-Macromolecule #2: Cyclin-A2
Macromolecule | Name: Cyclin-A2 / type: protein_or_peptide / ID: 2 / Details: Bovine cyclin A2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 30.119799 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGVNEVPDYH EDIHTYLREM EVKCKPKVGY MKKQPDITNS MRAILVDWLV EVGEEYKLQN ETLHLAVNYI DRFLSSMSVL RGKLQLVGT AAMLLASKFE EIYPPEVAEF VYITDDTYTK KQVLRMEHLV LKVLAFDLAA PTINQFLTQY FLHQQPANCK V ESLAMFLG ...String: MGVNEVPDYH EDIHTYLREM EVKCKPKVGY MKKQPDITNS MRAILVDWLV EVGEEYKLQN ETLHLAVNYI DRFLSSMSVL RGKLQLVGT AAMLLASKFE EIYPPEVAEF VYITDDTYTK KQVLRMEHLV LKVLAFDLAA PTINQFLTQY FLHQQPANCK V ESLAMFLG ELSLIDADPY LKYLPSVIAA AAFHLALYTV TGQSWPESLV QKTGYTLETL KPCLLDLHQT YLRAPQHAQQ SI REKYKNS KYHGVSLLNP PETLNV UniProtKB: Cyclin-A2 |
-Macromolecule #3: M-phase inducer phosphatase 1
Macromolecule | Name: M-phase inducer phosphatase 1 / type: protein_or_peptide / ID: 3 Details: M-phase inducer phosphatase 1 (CDC25A) catalytic domain Number of copies: 1 / Enantiomer: LEVO / EC number: protein-tyrosine-phosphatase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.533123 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SMVIGDFSKG YLFHTVAGKH QDLKYISPEI MASVLNGKFA NLIKEFVIID CRYPYEYEGG HIKGAVNLHM EEEVEDFLLK KPIVPTDGK RVIVVFHSEF SSERGPRMCR YVRERDRLGN EYPKLHYPEL YVLKGGYKEF FMKCQSYCEP PSYRPMHHED F KEDLKKFR TKSRTWAGEK SKREMYSRLK KL UniProtKB: M-phase inducer phosphatase 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: 50 mM HEPES, 200 mM NaCl, 1 mM DTT, pH 7.4 | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa Details: Grids were glow discharged for 1min at 20 mAmp/0.26 mBar | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.92 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo |
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Details | A model was generated using ModelAngelo. Initial local fitting was performed in ChimerX followed by real space refinement in Phenix and manual fitting in coot. |
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 144 |
Output model | PDB-8roz: |