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- EMDB-54971: Cryo-EM structure of CAK-CDK1-cyclin B1 -

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Entry
Database: EMDB / ID: EMD-54971
TitleCryo-EM structure of CAK-CDK1-cyclin B1
Map data
Sample
  • Complex: CAK-CDK1-cyclin B1 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK-activating kinase assembly factor MAT1
      • Protein or peptide: Cyclin-H
      • Protein or peptide: Cyclin-dependent kinase 7
    • Complex: CDK1-cyclin B1
      • Protein or peptide: Cyclin-dependent kinase 1
      • Protein or peptide: G2/mitotic-specific cyclin-B1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsComplex / cell cycle / kinase / TRANSFERASE
Function / homology
Function and homology information


regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of chromosome condensation / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation ...regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of chromosome condensation / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / E2F-enabled inhibition of pre-replication complex formation / G2/M DNA replication checkpoint / microtubule cytoskeleton organization involved in mitosis / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / MASTL Facilitates Mitotic Progression / positive regulation of mRNA 3'-end processing / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of attachment of spindle microtubules to kinetochore / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / : / patched binding / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / cyclin A2-CDK1 complex / Phosphorylation of Emi1 / Transcriptional regulation by RUNX2 / ventricular system development / tissue regeneration / Phosphorylation of the APC/C / Nuclear Pore Complex (NPC) Disassembly / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / outer kinetochore / protein localization to kinetochore / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / adult heart development / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cellular response to fatty acid / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / chromosome condensation / digestive tract development / oocyte maturation / [RNA-polymerase]-subunit kinase / centrosome cycle / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator activity / response to copper ion / mitotic metaphase chromosome alignment / MAPK3 (ERK1) activation / response to amine / cyclin-dependent protein kinase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / 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 / G1/S-Specific Transcription / mRNA Capping / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / ubiquitin-like protein ligase binding / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / peptidyl-threonine phosphorylation / RNA polymerase II transcribes snRNA genes / protein deubiquitination / positive regulation of G2/M transition of mitotic cell cycle / response to cadmium ion / cyclin-dependent kinase / ATP-dependent activity, acting on DNA / response to mechanical stimulus / cyclin-dependent protein serine/threonine kinase activity / Tat-mediated elongation of the HIV-1 transcript / response to axon injury / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Formation of HIV-1 elongation complex containing HIV-1 Tat / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / positive regulation of cardiac muscle cell proliferation / cyclin-dependent protein kinase holoenzyme complex
Similarity search - Function
: / CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / : ...: / CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / 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 / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 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 1 / G2/mitotic-specific cyclin-B1 / Cyclin-dependent kinase 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCushing VI / Greber BJ / McGeoch AJS / Feng J / Davey NE / Williams SL
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
The Institute of Cancer Research (ICR) United Kingdom
Cancer Research UKC68484/A28159 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
DepositionSep 2, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54971.png

Downloads & links

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Map

FileDownload / File: emd_54971.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 170 pix.
= 238. Å		1.4 Å/pix.
x 170 pix.
= 238. Å		1.4 Å/pix.
x 170 pix.
= 238. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.07714028 - 0.11765564
Average (Standard dev.)0.00003738335 (±0.004004136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54971_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_54971_half_map_1.map
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Half map: #1

Fileemd_54971_half_map_2.map
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Sample components

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Entire : CAK-CDK1-cyclin B1 complex

EntireName: CAK-CDK1-cyclin B1 complex
Components
  • Complex: CAK-CDK1-cyclin B1 complex
    • Complex: CDK-activating kinase (CAK)
      • Protein or peptide: CDK-activating kinase assembly factor MAT1
      • Protein or peptide: Cyclin-H
      • Protein or peptide: Cyclin-dependent kinase 7
    • Complex: CDK1-cyclin B1
      • Protein or peptide: Cyclin-dependent kinase 1
      • Protein or peptide: G2/mitotic-specific cyclin-B1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CAK-CDK1-cyclin B1 complex

SupramoleculeName: CAK-CDK1-cyclin B1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: CDK-activating kinase (CAK) in complex with CDK1-cyclin B1 in the presence of nucleotide analogue AMP-PNP
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82 KDa

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Supramolecule #2: CDK-activating kinase (CAK)

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

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Supramolecule #3: CDK1-cyclin B1

SupramoleculeName: CDK1-cyclin B1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Details: CDK1-cyclin B1 complex bound to nucleotide analogue AMP-PNP
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CDK-activating kinase assembly factor MAT1

MacromoleculeName: CDK-activating kinase assembly factor MAT1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.13234 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ...String:
MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ALEVERQENE QRRLFIQKEE QLQQILKRKN KQAFLDELES SDLPVALLLA QHKDRSTQLE MQLEKPKPVK PV TFSTGIK MGQHISLAPI HKLEEALYEY QPLQIETYGP HVPELEMLGR LGYLNHVRAA SPQDLAGGYT SSLACHRALQ DAF SGLFWQ PS

UniProtKB: CDK-activating kinase assembly factor MAT1

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Macromolecule #2: Cyclin-H

MacromoleculeName: Cyclin-H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.721508 KDa
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 #3: Cyclin-dependent kinase 7

MacromoleculeName: Cyclin-dependent kinase 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.65107 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ ...String:
MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ GLEYLHQHWI LHRDLKPNNL LLDENGVLKL ADFGLAKSFG SPNRAYTHQV VTRWYRAPEL LFGARMYGVG VD MWAVGCI LAELLLRVPF LPGDSDLDQL TRIFETLGTP TEEQWPDMCS LPDYVTFKSF PGIPLHHIFS AAGDDLLDLI QGL FLFNPC ARITATQALK MKYFSNRPGP TPGCQLPRPN CPVETLKEQS NPALAIKRKR TEALEQGGLP KKLIF

UniProtKB: Cyclin-dependent kinase 7

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Macromolecule #4: Cyclin-dependent kinase 1

MacromoleculeName: Cyclin-dependent kinase 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.651902 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPMGSMEDYT KIEKIGEGTY GVVYKGRHKT TGQVVAMKKI RLESEEEGVP STAIREISLL KELRHPNIVS LQDVLMQDSR LYLIFEFLS MDLKKYLDSI PPGQYMDSSL VKSYLYQILQ GIVFCHSRRV LHRDLKPQNL LIDDKGTIKL ADFGLARAFG I PIRVY(TPO)HE ...String:
GPMGSMEDYT KIEKIGEGTY GVVYKGRHKT TGQVVAMKKI RLESEEEGVP STAIREISLL KELRHPNIVS LQDVLMQDSR LYLIFEFLS MDLKKYLDSI PPGQYMDSSL VKSYLYQILQ GIVFCHSRRV LHRDLKPQNL LIDDKGTIKL ADFGLARAFG I PIRVY(TPO)HE VVTLWYRSPE VLLGSARYST PVDIWSIGTI FAELATKKPL FHGDSEIDQL FRIFRALGTP NNEVWPEV E SLQDYKNTFP KWKPGSLASH VKNLDENGLD LLSKMLIYDP AKRISGKMAL NHPYFNDLDN QIKKM

UniProtKB: Cyclin-dependent kinase 1

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Macromolecule #5: G2/mitotic-specific cyclin-B1

MacromoleculeName: G2/mitotic-specific cyclin-B1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.800766 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMALRV TRNSKINAEN KAKINMAGAK RVPTAPAATS KPGLRPRTAL GDIGNKVSEQ LQAKMPMKKE AKPSATGKVI DKKLPKPLE KVPMLVPVPV SEPVPEPEPE PEPEPVKEEK LSPEPILVDT ASPSPMETSG CAPAEEDLCQ AFSDVILAVN D VDAEDGAD ...String:
GAMGSMALRV TRNSKINAEN KAKINMAGAK RVPTAPAATS KPGLRPRTAL GDIGNKVSEQ LQAKMPMKKE AKPSATGKVI DKKLPKPLE KVPMLVPVPV SEPVPEPEPE PEPEPVKEEK LSPEPILVDT ASPSPMETSG CAPAEEDLCQ AFSDVILAVN D VDAEDGAD PNLCSEYVKD IYAYLRQLEE EQAVRPKYLL GREVTGNMRA ILIDWLVQVQ MKFRLLQETM YMTVSIIDRF MQ NNCVPKK MLQLVGVTAM FIASKYEEMY PPEIGDFAFV TDNTYTKHQI RQMEMKILRA LNFGLGRPLP LHFLRRASKI GEV DVEQHT LAKYLMELTM LDYDMVHFPP SQIAAGAFCL ALKILDNGEW TPTLQHYLSY TEESLLPVMQ HLAKNVVMVN QGLT KHMTV KNKYATSKHA KISTLPQLNS ALVQDLAKAV AKV

UniProtKB: G2/mitotic-specific cyclin-B1

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Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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

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 GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 14030 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware: (Name: cryoSPARC, RELION (ver. 5.0)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

53027

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 68765
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0)

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Atomic model buiding 1

Initial model
PDB IDChain

9qcv

source_name: PDB, initial_model_type: experimental model

5hq0

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9skq:
Cryo-EM structure of CAK-CDK1-cyclin B1

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