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- PDB-8p72: Cryo-EM structure of CAK in complex with inhibitor ICEC0768 -

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Basic information

Entry
Database: PDB / ID: 8p72
TitleCryo-EM structure of CAK in complex with inhibitor ICEC0768
Components
  • CDK-activating kinase assembly factor MAT1
  • Cyclin-H
  • Cyclin-dependent kinase 7
KeywordsTRANSFERASE / Kinase / Inhibitor / Transcription / Cell Cycle
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat S5 kinase activity / ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase ...RNA polymerase II CTD heptapeptide repeat S5 kinase activity / ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator 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 / mRNA Capping / RNA Polymerase I Transcription Initiation / regulation of G1/S transition of mitotic cell cycle / RNA polymerase II transcribes snRNA genes / ATP-dependent activity, acting on DNA / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of smooth muscle cell proliferation / RNA polymerase II CTD heptapeptide repeat kinase activity / male germ cell nucleus / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / G1/S transition of mitotic cell cycle / response to calcium ion / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / fibrillar center / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / kinase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription by RNA polymerase II / protein kinase activity / regulation of cell cycle / protein stabilization / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / Cyclin/Cyclin-like subunit Ssn8 / Ubiquitin interacting motif ...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/Cyclin-like subunit Ssn8 / 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 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsCushing, V.I. / Koh, A.F. / Feng, J. / Jurgaityte, K. / Bahl, A.K. / Ali, S. / Kotecha, A. / Greber, B.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design.
Authors: Victoria I Cushing / Adrian F Koh / Junjie Feng / Kaste Jurgaityte / Alexander Bondke / Sebastian H B Kroll / Marion Barbazanges / Bodo Scheiper / Ash K Bahl / Anthony G M Barrett / Simak ...Authors: Victoria I Cushing / Adrian F Koh / Junjie Feng / Kaste Jurgaityte / Alexander Bondke / Sebastian H B Kroll / Marion Barbazanges / Bodo Scheiper / Ash K Bahl / Anthony G M Barrett / Simak Ali / Abhay Kotecha / Basil J Greber /
Abstract: Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to ...Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.
History
DepositionMay 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: CDK-activating kinase assembly factor MAT1
I: Cyclin-H
J: Cyclin-dependent kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6834
Polymers87,3193
Non-polymers3641
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 10234.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P51948
#2: Protein Cyclin-H / MO15-associated protein / p34 / p37


Mass: 37721.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P51946
#3: Protein Cyclin-dependent kinase 7 / 39 kDa protein kinase / p39 Mo15 / CDK-activating kinase 1 / Cell division protein kinase 7 / ...39 kDa protein kinase / p39 Mo15 / CDK-activating kinase 1 / Cell division protein kinase 7 / Serine/threonine-protein kinase 1 / TFIIH basal transcription factor complex kinase subunit


Mass: 39362.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK7, CAK, CAK1, CDKN7, MO15, STK1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P50613, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#4: Chemical ChemComp-X2Z / ~{N}7-(phenylmethyl)-~{N}5-[(3~{S})-piperidin-3-yl]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine


Mass: 364.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CDK-activating kinase / Type: COMPLEX
Details: CAK in complex with non-covalent inhibitor ICEC0768
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.085 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMPotassium chlorideKCl1
22 mMMagnesium chlorideMgCl21
320 mMHEPES-KOH1
45 mMBeta-mercaptoethanol1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 245614 X / Nominal defocus max: 1700 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5583
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv3.3.1particle selection
2EPUimage acquisition
4RELION4.0 betaCTF correction
5cryoSPARCv3.3.1CTF correction
8UCSF ChimeraX1.2.5model fitting
10PHENIX1.20.1model refinement
11RELION4.0 betainitial Euler assignment
12RELION4.0 betafinal Euler assignment
13RELION4.0 betaclassification
14RELION4.0 beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334554 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8ORM

8orm


Accession code: 8ORM / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035227
ELECTRON MICROSCOPYf_angle_d0.5847074
ELECTRON MICROSCOPYf_dihedral_angle_d5.082696
ELECTRON MICROSCOPYf_chiral_restr0.041776
ELECTRON MICROSCOPYf_plane_restr0.005903

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