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- EMDB-53204: Cryo-EM structure of CDK2-cyclin A bound to OTS964 -

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Basic information

Entry
Database: EMDB / ID: EMD-53204
TitleCryo-EM structure of CDK2-cyclin A bound to OTS964
Map dataPost-processed (sharpened, filtered) cryo-EM map.
Sample
  • Complex: CDK2-cyclin A2-OTS964 complex
    • Protein or peptide: Cyclin-A2
    • Protein or peptide: Cyclin-dependent kinase 2
  • Ligand: OTS964
  • Ligand: water
Keywordskinase / cyclin-dependent kinase / inhibitor / CELL CYCLE
Function / homology
Function and homology information


cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon ...cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / regulation of heterochromatin organization / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / cellular response to insulin-like growth factor stimulus / 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 / X chromosome / PTK6 Regulates Cell Cycle / 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 / regulation of DNA replication / centrosome duplication / microtubule organizing center / G0 and Early G1 / cochlea development / animal organ regeneration / Telomere Extension By Telomerase / Activation of the pre-replicative 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 / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / 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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of G2/M transition of mitotic cell cycle / condensed chromosome / cellular response to platelet-derived growth factor stimulus / mitotic G1 DNA damage checkpoint signaling / negative regulation of protein localization to chromatin / cellular response to nitric oxide / post-translational protein modification / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / peptidyl-serine phosphorylation / male germ cell nucleus / meiotic cell cycle / cellular response to estradiol stimulus / potassium ion transport / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / CDK-mediated phosphorylation and removal of Cdc6 / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / G2/M transition of mitotic cell cycle / SCF(Skp2)-mediated degradation of p27/p21 / positive regulation of fibroblast proliferation / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / regulation of gene expression / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / Ras protein signal transduction / DNA replication / chromosome, telomeric region / endosome / Ub-specific processing proteases / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation
Similarity search - Function
Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / 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-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsMcGeoch AJS / Cushing VI / Cronin NB / Alfieri C / Greber BJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation
Authors: McGeoch AJS / Cushing VI / Roumeliotis TI / Cronin NB / Alfieri C / Greber BJ / Choudhary J
History
DepositionMar 19, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53204.png

Downloads & links

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Map

FileDownload / File: emd_53204.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed (sharpened, filtered) cryo-EM map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 192 pix.
= 195.84 Å		1.02 Å/pix.
x 192 pix.
= 195.84 Å		1.02 Å/pix.
x 192 pix.
= 195.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.07346694 - 0.11391803
Average (Standard dev.)0.000008924781 (±0.003939232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 195.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53204_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered cryo-EM half-map from refinement.

Fileemd_53204_half_map_1.map
AnnotationUnfiltered cryo-EM half-map from refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered cryo-EM half-map from refinement.

Fileemd_53204_half_map_2.map
AnnotationUnfiltered cryo-EM half-map from refinement.
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-cyclin A2-OTS964 complex

EntireName: CDK2-cyclin A2-OTS964 complex
Components
  • Complex: CDK2-cyclin A2-OTS964 complex
    • Protein or peptide: Cyclin-A2
    • Protein or peptide: Cyclin-dependent kinase 2
  • Ligand: OTS964
  • Ligand: water

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Supramolecule #1: CDK2-cyclin A2-OTS964 complex

SupramoleculeName: CDK2-cyclin A2-OTS964 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80 KDa

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Macromolecule #1: Cyclin-A2

MacromoleculeName: Cyclin-A2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.867805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVT VPPWKANSKQ PAFTIHVDEA EKEAQKKPAE SQKIEREDAL AFNSAISLPG PRKPLVPLDY PMDGSFESPH T MDMSIVLE ...String:
SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVT VPPWKANSKQ PAFTIHVDEA EKEAQKKPAE SQKIEREDAL AFNSAISLPG PRKPLVPLDY PMDGSFESPH T MDMSIVLE DEKPVSVNEV PDYHEDIHTY LREMEVKCKP KVGYMKKQPD ITNSMRAILV DWLVEVGEEY KLQNETLHLA VN YIDRFLS SMSVLRGKLQ LVGTAAMLLA SKFEEIYPPE VAEFVYITDD TYTKKQVLRM EHLVLKVLTF DLAAPTVNQF LTQ YFLHQQ PANCKVESLA MFLGELSLID ADPYLKYLPS VIAGAAFHLA LYTVTGQSWP ESLIRKTGYT LESLKPCLMD LHQT YLKAP QHAQQSIREK YKNSKYHGVS LLNPPETLNL

UniProtKB: Cyclin-A2

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Macromolecule #2: Cyclin-dependent kinase 2

MacromoleculeName: Cyclin-dependent kinase 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.24875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMENFQKV EKIGEGTYGV VYKARNKLTG EVVALKKIRL DTETEGVPST AIREISLLKE LNHPNIVKLL DVIHTENKLY LVFEFLHQD LKKFMDASAL TGIPLPLIKS YLFQLLQGLA FCHSHRVLHR DLKPQNLLIN TEGAIKLADF GLARAFGVPV R TYTHEVVT ...String:
SNAMENFQKV EKIGEGTYGV VYKARNKLTG EVVALKKIRL DTETEGVPST AIREISLLKE LNHPNIVKLL DVIHTENKLY LVFEFLHQD LKKFMDASAL TGIPLPLIKS YLFQLLQGLA FCHSHRVLHR DLKPQNLLIN TEGAIKLADF GLARAFGVPV R TYTHEVVT LWYRAPEILL GCKYYSTAVD IWSLGCIFAE MVTRRALFPG DSEIDQLFRI FRTLGTPDEV VWPGVTSMPD YK PSFPKWA RQDFSKVVPP LDEDGRSLLS QMLHYDPNKR ISAKAALAHP FFQDVTKPVP HLRL

UniProtKB: Cyclin-dependent kinase 2

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Macromolecule #3: OTS964

MacromoleculeName: OTS964 / type: ligand / ID: 3 / Number of copies: 1 / Formula: NK3
Molecular weightTheoretical: 392.514 Da
Chemical component information

ChemComp-NK3:
OTS964

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 55 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.4 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
40.0 mMHEPES-KOH
200.0 mMPotassium chlorideKCl
2.0 mMMagnesium chlorideMgCl2
5.0 mMbeta-mercaptoethanol
0.025 mMOTS964
0.2 mM21-mer cryo-peptide
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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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) / Number real images: 15468 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: cryoSPARC (ver. 4.4.1), RELION (ver. 5.0-beta))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Number images used: 503775
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 5.0-beta)

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Atomic model buiding 1

Initial modelPDB ID:

6sxa


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qjj:
Cryo-EM structure of CDK2-cyclin A bound to OTS964

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