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- PDB-31zn: Structure of CDK11-cyclin L-SAP30BP in complex with IACS-054647 -

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Basic information

Entry
Database: PDB / ID: 31zn
TitleStructure of CDK11-cyclin L-SAP30BP in complex with IACS-054647
Components
  • Cyclin-L2
  • Isoform 7 of Cyclin-dependent kinase 11B
  • SAP30-binding protein
KeywordsTRANSFERASE / Kinase / small molecule / splicing / transcription / inhibitor
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat S2 kinase activity / cyclin L-CDK11 complex / mitotic sister chromatid cohesion, centromeric / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / regulation of mRNA processing / regulation of centrosome cycle / regulation of mRNA splicing, via spliceosome / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity ...RNA polymerase II CTD heptapeptide repeat S2 kinase activity / cyclin L-CDK11 complex / mitotic sister chromatid cohesion, centromeric / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / regulation of mRNA processing / regulation of centrosome cycle / regulation of mRNA splicing, via spliceosome / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of RNA splicing / cyclin-dependent protein kinase holoenzyme complex / chromosome, centromeric region / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Recruitment of mitotic centrosome proteins and complexes / RNA splicing / regulation of cell growth / response to virus / NoRC negatively regulates rRNA expression / mRNA processing / mitotic cell cycle / chromosome / regulation of apoptotic process / regulation of cell cycle / protein kinase activity / protein phosphorylation / 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 / 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
: / Cyclin-dependent kinase 11B / Cyclin-L2 / SAP30-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMcGeoch, A.J.S. / Greber, B.J. / Sheltzer, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Institute of Cancer Research (ICR) United Kingdom
CitationJournal: To Be Published
Title: Structure of CDK11-cyclin L-SAP30BP in complex with IACS-054647
Authors: McGeoch, A.J.S. / Greber, B.J. / Sheltzer, J.M.
History
DepositionJun 30, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: SAP30-binding protein
B: Isoform 7 of Cyclin-dependent kinase 11B
C: Cyclin-L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1654
Polymers119,8483
Non-polymers3171
Water00
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 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High5 / References: UniProt: Q9UHR5
#2: Protein Isoform 7 of 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: 49970.613 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 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High5 / References: UniProt: P21127, cyclin-dependent kinase
#3: 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 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High5 / References: UniProt: Q96S94
#4: Chemical ChemComp-A1KC9 / 4-[8-[[(3~{S})-piperidin-3-yl]amino]imidazo[1,2-a]pyridin-6-yl]benzenecarbonitrile


Mass: 317.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N5 / Feature type: SUBJECT OF INVESTIGATION
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: CDK11-cyclin L-SAP30BP bound by IACS-054647 / 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) / Strain: High5
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
140 mMHEPES-KOH1
2200 mMPotassium chlorideKCl1
32 mMMagnesium chlorideMgCl21
45 mMbeta-mercaptoethanol1
525 uMIACS-0546471
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Tergeo-EM plasma cleaner (PIE Scientific) / Grid 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: 5 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12610
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5.0.6particle selection
2EPU3.8.1image acquisition
4cryoSPARC5.0.6CTF correction
5RELION5.0.1CTF correction
8UCSF ChimeraX1.1model fitting
9Coot0.9.6model fitting
11PHENIX1.21.2_5419model refinement
12cryoSPARC5.0.6initial Euler assignment
13RELION5.0.1final Euler assignment
14RELION5.0.1classification
15RELION5.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7674974
Details: Three independent picking methods employed; each method picked approx. 5-8 million particles; figure above is the greatest number picked by any of the three methods.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 363221 / Algorithm: FOURIER SPACE / Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 9QKT

9qkt


Accession code: 9QKT / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065449
ELECTRON MICROSCOPYf_angle_d0.6017356
ELECTRON MICROSCOPYf_dihedral_angle_d6.914731
ELECTRON MICROSCOPYf_chiral_restr0.046803
ELECTRON MICROSCOPYf_plane_restr0.005934

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