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- EMDB-65363: CDK11B ternary complex bound to AT7519 -

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Basic information

Entry
Database: EMDB / ID: EMD-65363
TitleCDK11B ternary complex bound to AT7519
Map dataprimary map
Sample
  • Complex: Ternary complex of CDK11B, Cyclin L1 and SAP30BP bound to AT7519
    • Protein or peptide: Cyclin-dependent kinase 11B
    • Protein or peptide: Cyclin-L1
    • Protein or peptide: SAP30-binding protein
  • Ligand: 4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyrazole-3-carboxamide
KeywordsAT7519 / CDK11 / Cyclin L1 / SAP30BP / SPLICING
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
Cyclin-dependent kinase 11B / SAP30-binding protein / Cyclin-L1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYang Y / Wang L / Zheng Z / Zhan X / Shi Y
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65363.png

Downloads & links

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Map

FileDownload / File: emd_65363.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 320 pix.
= 182.4 Å		0.57 Å/pix.
x 320 pix.
= 182.4 Å		0.57 Å/pix.
x 320 pix.
= 182.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0144
Minimum - Maximum-0.060733043 - 0.10374943
Average (Standard dev.)-0.000095578915 (±0.0028979229)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 182.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_65363_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65363_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of CDK11B, Cyclin L1 and SAP30BP bound to AT7519

EntireName: Ternary complex of CDK11B, Cyclin L1 and SAP30BP bound to AT7519
Components
  • Complex: Ternary complex of CDK11B, Cyclin L1 and SAP30BP bound to AT7519
    • Protein or peptide: Cyclin-dependent kinase 11B
    • Protein or peptide: Cyclin-L1
    • Protein or peptide: SAP30-binding protein
  • Ligand: 4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyrazole-3-carboxamide

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Supramolecule #1: Ternary complex of CDK11B, Cyclin L1 and SAP30BP bound to AT7519

SupramoleculeName: Ternary complex of CDK11B, Cyclin L1 and SAP30BP bound to AT7519
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Cyclin-dependent kinase 11B

MacromoleculeName: Cyclin-dependent kinase 11B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.171027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGRGAMGALQ GCRSVEEFQC LNRIEEGTYG VVYRAKDKKT DEIVALKRLK MEKEKEGFPI TSLREINTIL KAQHPNIVT VREIVVGSNM DKIYIVMNYV EHDLKSLMET MKQPFLPGEV KTLMIQLLRG VKHLHDNWIL HRDLKTSNLL L SHAGILKV ...String:
MADYKDDDDK SGRGAMGALQ GCRSVEEFQC LNRIEEGTYG VVYRAKDKKT DEIVALKRLK MEKEKEGFPI TSLREINTIL KAQHPNIVT VREIVVGSNM DKIYIVMNYV EHDLKSLMET MKQPFLPGEV KTLMIQLLRG VKHLHDNWIL HRDLKTSNLL L SHAGILKV GDFGLAREYG (SEP)PLKAY(TPO)PVV VTLWYRAPEL LLGAKEYSTA VDMWSVGCIF GELLTQKPLF PGKS EIDQI NKVFKDLGTP SEKIWPGYSE LPAVKKMTFS EHPYNNLRKR FGALLSDQGF DLMNKFLTYF PGRRISAEDG LKHEY FRET PLPIDPSMFP KLVEKY

UniProtKB: Cyclin-dependent kinase 11B

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Macromolecule #2: Cyclin-L1

MacromoleculeName: Cyclin-L1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.238141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASGPHSTAT AAAAASSAAP SAGGSSSGTT TTTTTTTGGI LIGDRLYSEV SLTIDHSLIP EERLSPTPSM QDGLDLPSET DLRILGCEL IQAAGILLRL PQVAMATGQV LFHRFFYSKS FVKHSFEIVA MACINLASKI EEAPRRIRDV INVFHHLRQL R GKRTPSPL ...String:
MASGPHSTAT AAAAASSAAP SAGGSSSGTT TTTTTTTGGI LIGDRLYSEV SLTIDHSLIP EERLSPTPSM QDGLDLPSET DLRILGCEL IQAAGILLRL PQVAMATGQV LFHRFFYSKS FVKHSFEIVA MACINLASKI EEAPRRIRDV INVFHHLRQL R GKRTPSPL ILDQNYINTK NQVIKAERRV LKELGFCVHV KHPHKIIVMY LQVLECERNQ TLVQTAWNYM NDSLRTNVFV RF QPETIAC ACIYLAARAL QIPLPTRPHW FLLFGTTEEE IQEICIETLR LYTRKKPNYE LLEKEVEKRK VALQEAKLKA KGL NPDGRI PGLIWSHPQF EKGGGSGGGG GSGGGSGGSS AWSHPQFEK

UniProtKB: Cyclin-L1

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Macromolecule #3: SAP30-binding protein

MacromoleculeName: SAP30-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.056547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSENLYFQG MAGKKNVLSS LAVYAEDSEP ESDGEAGIEA VGSTAEEKGG LVSDAYGEDD FSRLGGDEDG YEEEEDENSR QSEDDDSET EKPEADDPKD NTEAEKRDPQ ELVASFSERV RNMSPDEIKI PPEPPGRCSN HLQDKIQKLY ERKIKEGMDM N YIIQRKKE ...String:
MGSENLYFQG MAGKKNVLSS LAVYAEDSEP ESDGEAGIEA VGSTAEEKGG LVSDAYGEDD FSRLGGDEDG YEEEEDENSR QSEDDDSET EKPEADDPKD NTEAEKRDPQ ELVASFSERV RNMSPDEIKI PPEPPGRCSN HLQDKIQKLY ERKIKEGMDM N YIIQRKKE FRNPSIYEKL IQFCAIDELG TNYPKDMFDP HGWSEDSYYE ALAKAQKIEM DKLEKAKKER TKIEFVTGTK KG TTTNATS TTTTTASTAV ADAQKRKSKW DSAIPVTTIA QPTILTTTAT LPAVVTVTTS ASGSKTTVIS AVGTIVKNAK Q

UniProtKB: SAP30-binding protein

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Macromolecule #4: 4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyraz...

MacromoleculeName: 4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyrazole-3-carboxamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: LZE
Molecular weightTheoretical: 382.244 Da
Chemical component information

ChemComp-LZE:
4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyrazole-3-carboxamide

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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

BufferpH: 7.5 / Details: 20 mM HEPES, 150 mM NaCl, 1.5 mM MgCl2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111653
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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