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- PDB-9vuh: CDK11B ternary complex bound to AT7519 -

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Basic information

Entry
Database: PDB / ID: 9vuh
TitleCDK11B ternary complex bound to AT7519
Components
  • Cyclin-L1
  • Cyclin-dependent kinase 11B
  • SAP30-binding protein
KeywordsSPLICING / AT7519 / CDK11 / Cyclin L1 / SAP30BP
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 / chromosome, centromeric region / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / Recruitment of mitotic centrosome proteins and complexes / RNA splicing / regulation of cell growth / NoRC negatively regulates rRNA expression / response to virus / mRNA processing / mitotic cell cycle / chromosome / regulation of apoptotic process / protein phosphorylation / protein kinase activity / regulation of cell cycle / nuclear speck / nuclear body / 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
Chem-LZE / Cyclin-dependent kinase 11B / SAP30-binding protein / Cyclin-L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYang, Y. / Wang, L. / Zheng, Z. / Zhan, X. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: To Be Published
Title: Identification of An Anti-cancer Pre-clinical Candidate as A Potent Inhibitor of RNA Splicing
Authors: Wang, L. / Yang, Y. / Zheng, Z. / Zhan, X. / Shi, Y.
History
DepositionJul 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 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: Cyclin-dependent kinase 11B
B: Cyclin-L1
C: SAP30-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8484
Polymers113,4663
Non-polymers3821
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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: 38171.027 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: Homo sapiens (human) / References: UniProt: P21127, cyclin-dependent kinase
#2: Protein Cyclin-L1 / Cyclin-L


Mass: 40238.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNL1, BM-001, UNQ530/PRO1073 / Production host: Homo sapiens (human) / References: UniProt: Q9UK58
#3: Protein SAP30-binding protein / Transcriptional regulator protein HCNGP


Mass: 35056.547 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: Homo sapiens (human) / References: UniProt: Q9UHR5
#4: Chemical ChemComp-LZE / 4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyrazole-3-carboxamide


Mass: 382.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17Cl2N5O2 / 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: Ternary complex of CDK11B, Cyclin L1 and SAP30BP bound to AT7519
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES, 150 mM NaCl, 1.5 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111653 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035316
ELECTRON MICROSCOPYf_angle_d0.5317178
ELECTRON MICROSCOPYf_dihedral_angle_d5.146703
ELECTRON MICROSCOPYf_chiral_restr0.04789
ELECTRON MICROSCOPYf_plane_restr0.004910

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