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- EMDB-52759: Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP (locally... -

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Entry
Database: EMDB / ID: EMD-52759
TitleCryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP (locally refined map)
Map dataPost-processed, sharpened map.
Sample
  • Complex: CAK-CDK2-cyclin A2 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK7
      • Protein or peptide: Cyclin H
      • Protein or peptide: MAT1
    • Complex: CDK2-cyclin A2
      • Protein or peptide: CDK2
      • Protein or peptide: Cyclin A2
KeywordsComplex / cell cycle / kinase / TRANSFERASE
Function / homology
Function and homology information


: / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus ...: / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / male pronucleus / female pronucleus / cellular response to cocaine / [RNA-polymerase]-subunit kinase / response to glucagon / RNA Polymerase I Transcription Termination / positive regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / 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 / Y chromosome / cyclin-dependent protein kinase activity / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / X chromosome / mRNA Capping / 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 / regulation of DNA replication / telomere maintenance in response to DNA damage / microtubule organizing center / centrosome duplication / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / G0 and Early G1 / cochlea development / RNA polymerase II transcribes snRNA genes / Telomere Extension By Telomerase / animal organ regeneration / Activation of the pre-replicative complex / cyclin-dependent kinase / ATP-dependent activity, acting on DNA / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Activation of ATR in response to replication stress / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Cyclin E associated events during G1/S transition / Formation of HIV elongation complex in the absence of HIV Tat / 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 / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / cellular response to platelet-derived growth factor stimulus / mitotic G1 DNA damage checkpoint signaling / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cellular response to nitric oxide / post-translational protein modification / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RNA Polymerase I Promoter Escape / cellular response to estradiol stimulus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / NoRC negatively regulates rRNA expression / potassium ion transport
Similarity search - Function
CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / : / Cyclin, C-terminal domain / : / Cyclins signature. ...CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin/Cyclin-like subunit Ssn8 / 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 / Cyclin-dependent kinase 7 / Cyclin-H / Isoform 1 of CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsCushing VI / Greber BJ / McGeoch AJS / Feng J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
The Institute of Cancer Research (ICR) United Kingdom
CitationJournal: Science / Year: 2025
Title: Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase.
Authors: Victoria I Cushing / Amy J S McGeoch / Sophie L Williams / Theodoros I Roumeliotis / Junjie Feng / Lucy M Dan / Jyoti S Choudhary / Norman E Davey / Basil J Greber /
Abstract: Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation ...Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation of CDKs on a conserved threonine residue within the regulatory T-loop. However, structural data illuminating the mechanism by which the CAK recognizes and activates CDKs have remained elusive. In this study, we determined high-resolution structures of the CAK in complex with CDK2 and CDK2-cyclin A2 by cryogenic electron microscopy. Our structures reveal a T-loop-independent kinase-kinase interface with contributions from both kinase lobes. Computational analysis and structures of the CAK in complex with CDK1-cyclin B1 and CDK11 indicate that these structures represent the general architecture of CAK-CDK complexes. These results advance our mechanistic understanding of cell cycle regulation and kinase signaling cascades.
History
DepositionFeb 6, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52759.png

Downloads & links

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Map

FileDownload / File: emd_52759.map.gz / Format: CCP4 / Size: 48.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed, sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 234 pix.
= 255.42 Å		1.09 Å/pix.
x 234 pix.
= 255.42 Å		1.09 Å/pix.
x 234 pix.
= 255.42 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09154 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.08326162 - 0.15326571
Average (Standard dev.)0.00002337198 (±0.0038023973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions234234234
Spacing234234234
CellA=B=C: 255.42035 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52759_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map.

Fileemd_52759_half_map_1.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map.

Fileemd_52759_half_map_2.map
AnnotationUnfiltered half-map.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CAK-CDK2-cyclin A2 complex

EntireName: CAK-CDK2-cyclin A2 complex
Components
  • Complex: CAK-CDK2-cyclin A2 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK7
      • Protein or peptide: Cyclin H
      • Protein or peptide: MAT1
    • Complex: CDK2-cyclin A2
      • Protein or peptide: CDK2
      • Protein or peptide: Cyclin A2

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Supramolecule #1: CAK-CDK2-cyclin A2 complex

SupramoleculeName: CAK-CDK2-cyclin A2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: CDK-activating kinase (CAK) in complex with CDK2-cyclin A2 in the presence of the nucleotide analogue AMP-PNP. The deposited map is the result of local refinement using a mask encompassing ...Details: CDK-activating kinase (CAK) in complex with CDK2-cyclin A2 in the presence of the nucleotide analogue AMP-PNP. The deposited map is the result of local refinement using a mask encompassing only the CDK2-cyclin A2 portion of the complex.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83 KDa

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Supramolecule #2: CDK-activating kinase (CAK)

SupramoleculeName: CDK-activating kinase (CAK) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#5 / Details: CAK complex bound to nucleotide analogue AMP-PNP
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: CDK2-cyclin A2

SupramoleculeName: CDK2-cyclin A2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Details: CDK2-cyclin A2 complex bound to nucleotide analogue AMP-PNP
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CDK2

MacromoleculeName: CDK2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #2: Cyclin A2

MacromoleculeName: Cyclin A2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVTV PPWKANSKQP AFTIHVDEAE KEAQKKPAES QKIEREDALA FNSAISLPGP RKPLVPLDYP MDGSFESPHT MDMSIVLEDE ...String:
SNAMLGNSAP GPATREAGSA LLALQQTALQ EDQENINPEK AAPVQQPRTR AALAVLKSGN PRGLAQQQRP KTRRVAPLKD LPVNDEHVTV PPWKANSKQP AFTIHVDEAE KEAQKKPAES QKIEREDALA FNSAISLPGP RKPLVPLDYP MDGSFESPHT MDMSIVLEDE KPVSVNEVPD YHEDIHTYLR EMEVKCKPKV GYMKKQPDIT NSMRAILVDW LVEVGEEYKL QNETLHLAVN YIDRFLSSMS VLRGKLQLVG TAAMLLASKF EEIYPPEVAE FVYITDDTYT KKQVLRMEHL VLKVLTFDLA APTVNQFLTQ YFLHQQPANC KVESLAMFLG ELSLIDADPY LKYLPSVIAG AAFHLALYTV TGQSWPESLI RKTGYTLESL KPCLMDLHQT YLKAPQHAQQ SIREKYKNSK YHGVSLLNPP ETLNL

UniProtKB: Cyclin-A2

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Macromolecule #3: CDK7

MacromoleculeName: CDK7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIKL GHRSEAKDGI NRTALREIKL LQELSHPNII GLLDAFGHKS NISLVFDFME TDLEVIIKDN SLVLTPSHIK AYMLMTLQGL ...String:
MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIKL GHRSEAKDGI NRTALREIKL LQELSHPNII GLLDAFGHKS NISLVFDFME TDLEVIIKDN SLVLTPSHIK AYMLMTLQGL EYLHQHWILH RDLKPNNLLL DENGVLKLAD FGLAKSFGSP NRAYTHQVVT RWYRAPELLF GARMYGVGVD MWAVGCILAE LLLRVPFLPG DSDLDQLTRI FETLGTPTEE QWPDMCSLPD YVTFKSFPGI PLHHIFSAAG DDLLDLIQGL FLFNPCARIT ATQALKMKYF SNRPGPTPGC QLPRPNCPVE TLKEQSNPAL AIKRKRTEAL EQGGLPKKLI F

UniProtKB: Cyclin-dependent kinase 7

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Macromolecule #4: Cyclin H

MacromoleculeName: Cyclin H / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: (ACE)MYHNSSQKR HWTFSSEEQL ARLRADANRK FRCKAVANGK VLPNDPVFLE PHEEMTLCKY YEKRLLEFCS VFKPAM PRS VVGTACMYFK RFYLNNSVME YHPRIIMLTC AFLACKVDEF NVSSPQFVGN LRESPLGQEK ALEQILEYEL LLIQQLN FH LIVHNPYRPF ...String:
(ACE)MYHNSSQKR HWTFSSEEQL ARLRADANRK FRCKAVANGK VLPNDPVFLE PHEEMTLCKY YEKRLLEFCS VFKPAM PRS VVGTACMYFK RFYLNNSVME YHPRIIMLTC AFLACKVDEF NVSSPQFVGN LRESPLGQEK ALEQILEYEL LLIQQLN FH LIVHNPYRPF EGFLIDLKTR YPILENPEIL RKTADDFLNR IALTDAYLLY TPSQIALTAI LSSASRAGIT MESYLSES L MLKENRTCLS QLLDIMKSMR NLVKKYEPPR SEEVAVLKQK LERCHSAELA LNVITKKRKG YEDDDYVSKK SKHEEEEWT DDDLVESL

UniProtKB: Cyclin-H

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Macromolecule #5: MAT1

MacromoleculeName: MAT1 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDKE VEIRKKVLKI YNKREEDFPS LREYNDFLEE VEEIVFNLTN NVDLDNTKKK MEIYQKENKD VIQKNKLKLT REQEELEEAL ...String:
MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDKE VEIRKKVLKI YNKREEDFPS LREYNDFLEE VEEIVFNLTN NVDLDNTKKK MEIYQKENKD VIQKNKLKLT REQEELEEAL EVERQENEQR RLFIQKEEQL QQILKRKNKQ AFLDELESSD LPVALLLAQH KDRSTQLEMQ LEKPKPVKPV TFSTGIKMGQ HISLAPIHKL EEALYEYQPL QIETYGPHVP ELEMLGRLGY LNHVRAASPQ DLAGGYTSSL ACHRALQDAF SGLFWQPS

UniProtKB: Isoform 1 of CDK-activating kinase assembly factor MAT1

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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: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMSodium chlorideNaCl
10.0 mMMagnesium chlorideMgCl2
0.5 mMAMP-PNP
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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 33998 / Average electron dose: 50.0 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: 2.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 130000
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, RELION (ver. 4.0)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 282506
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0)

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