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- PDB-9qkt: Cryo-EM structure of the CDK11B-cyclin L2-SAP30BP bound to OTS964... -

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Basic information

Entry
Database: PDB / ID: 9qkt
TitleCryo-EM structure of the CDK11B-cyclin L2-SAP30BP bound to OTS964 (conformation 1)
Components
  • Cyclin-L2
  • Cyclin-dependent kinase 11B
  • SAP30-binding protein
KeywordsSPLICING / kinase / cyclin-dependent kinase / inhibitor / transcription / molecular complex
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / regulation of mRNA processing / regulation of centrosome cycle / intermediate filament cytoskeleton / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of RNA splicing / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex ...mitotic sister chromatid cohesion, centromeric / regulation of mRNA processing / regulation of centrosome cycle / intermediate filament cytoskeleton / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of RNA splicing / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / Recruitment of mitotic centrosome proteins and complexes / regulation of cell growth / NoRC negatively regulates rRNA expression / response to virus / mitotic cell cycle / regulation of apoptotic process / protein phosphorylation / protein kinase activity / regulation of cell cycle / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
SAP30-binding protein / HCNGP-like protein / Cyclin-dependent kinase 11/PITSLRE, catalytic domain / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like ...SAP30-binding protein / HCNGP-like protein / Cyclin-dependent kinase 11/PITSLRE, catalytic domain / Cyclin-T2-like, C-terminal domain / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
OTS964 / Cyclin-dependent kinase 11B / Cyclin-L2 / SAP30-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMcGeoch, A.J.S. / Cushing, V.I. / Cronin, N.B. / Alfieri, C. / Greber, B.J.
Funding support United Kingdom, 1items
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, A.J.S. / Cushing, V.I. / Roumeliotis, T.I. / Cronin, N.B. / Alfieri, C. / Greber, B.J. / Choudhary, J.
History
DepositionMar 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAP30-binding protein
C: Cyclin-L2
B: Cyclin-dependent kinase 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3204
Polymers119,9283
Non-polymers3931
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein SAP30-binding protein / Transcriptional regulator protein HCNGP


Mass: 34186.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAP30BP, HCNGP, HTRG, HTRP / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UHR5
#2: Protein Cyclin-L2 / Paneth cell-enhanced expression protein


Mass: 35690.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNL2, SB138 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96S94
#3: Protein Cyclin-dependent kinase 11B / Cell division cycle 2-like protein kinase 1 / CLK-1 / Cell division protein kinase 11B / ...Cell division cycle 2-like protein kinase 1 / CLK-1 / Cell division protein kinase 11B / Galactosyltransferase-associated protein kinase p58/GTA / PITSLRE serine/threonine-protein kinase CDC2L1 / p58 CLK-1


Mass: 50050.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK11B, CDC2L1, CDK11, PITSLREA, PK58 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21127, cyclin-dependent kinase
#4: Chemical ChemComp-NK3 / OTS964


Mass: 392.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24N2O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: CDK11B-cyclin L2-SAP30BP-OTS964 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.12 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
140 mMHEPES-KOH1
2200 mMPotassium chlorideKCl1
32 mMMagnesium chlorideMgCl21
45 mMbeta-mercaptoethanol1
50.025 mMOTS9641
SpecimenConc.: 0.5 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: UltrAuFoil 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 / Nominal magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 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: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 13829
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUimage acquisition
4cryoSPARC4.4.1CTF correction
5RELION5.0-betaCTF correction
8UCSF ChimeraXmodel fitting
10RELION5.0-betainitial Euler assignment
11RELION5.0-betafinal Euler assignment
12RELION5.0-betaclassification
13RELION5.0-beta3D reconstruction
14PHENIX1.21rc1_4985model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286108 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Coordinates based on prior cryo-EM reconstruction of this complex.
Source name: Other / Type: experimental model
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035698
ELECTRON MICROSCOPYf_angle_d0.4717696
ELECTRON MICROSCOPYf_dihedral_angle_d4.587752
ELECTRON MICROSCOPYf_chiral_restr0.038836
ELECTRON MICROSCOPYf_plane_restr0.004977

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