[English] 日本語
Yorodumi
- EMDB-19408: Cryo-EM structure of CDK2-cyclin A in complex with CDC25A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19408
TitleCryo-EM structure of CDK2-cyclin A in complex with CDC25A
Map data
Sample
  • Complex: Trimeric complex of CDK2-cyclin A-CDC25A
    • Protein or peptide: Cyclin-dependent kinase 2
    • Protein or peptide: Cyclin-A2
    • Protein or peptide: M-phase inducer phosphatase 1
Keywordscell-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 / phosphoprotein phosphatase activity / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / 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 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 / : / meiotic cell cycle / positive regulation of DNA replication / protein tyrosine phosphatase activity / male germ cell nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / potassium ion transport / response to radiation / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular response to UV / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Regulation of TP53 Activity through Phosphorylation / cell population proliferation / transcription regulator complex / Ras protein signal transduction / 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 / DNA-templated transcription / centrosome / 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 / signal transduction / nucleoplasm
Similarity search - Function
M-phase inducer phosphatase / M-phase inducer phosphatase / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Rhodanese Homology Domain / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin ...M-phase inducer phosphatase / M-phase inducer phosphatase / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Rhodanese Homology Domain / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Cyclin, C-terminal domain / Cyclin_C / Rhodanese-like domain / Cyclin, N-terminal / Cyclin, N-terminal domain / 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 / Serine/Threonine protein kinases, catalytic domain / 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
Cyclin-dependent kinase 2 / Cyclin-A2 / M-phase inducer phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsRowland RJ / Noble MEM / Endicott JA
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V029142/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009738/1 United Kingdom
CitationJournal: 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
DepositionJan 12, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19408.png

Downloads & links

-
Map

FileDownload / File: emd_19408.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.6334735 - 0.9438938
Average (Standard dev.)0.00021430186 (±0.017006245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 237.59999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19408_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19408_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19408_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Trimeric complex of CDK2-cyclin A-CDC25A

EntireName: Trimeric complex of CDK2-cyclin A-CDC25A
Components
  • Complex: Trimeric complex of CDK2-cyclin A-CDC25A
    • Protein or peptide: Cyclin-dependent kinase 2
    • Protein or peptide: Cyclin-A2
    • Protein or peptide: M-phase inducer phosphatase 1

-
Supramolecule #1: Trimeric complex of CDK2-cyclin A-CDC25A

SupramoleculeName: Trimeric complex of CDK2-cyclin A-CDC25A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86 KDa

-
Macromolecule #1: Cyclin-dependent kinase 2

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.136449 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

MacromoleculeName: Cyclin-A2 / type: protein_or_peptide / ID: 2 / Details: Bovine cyclin A2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 30.119799 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.533123 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
200.0 mMNaClSalt
1.0 mMDTTDTT

Details: 50 mM HEPES, 200 mM NaCl, 1 mM DTT, pH 7.4
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.92 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4981705
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 670830
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: non-uniform refinement
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
DetailsA model was generated using ModelAngelo. Initial local fitting was performed in ChimerX followed by real space refinement in Phenix and manual fitting in coot.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 144
Output model

PDB-8roz:
Cryo-EM structure of CDK2-cyclin A in complex with CDC25A

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more