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- EMDB-58734: Structure of CDK11-cyclin L-SAP30BP in complex with IACS-054647 -

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Basic information

Entry
Database: EMDB / ID: EMD-58734
TitleStructure of CDK11-cyclin L-SAP30BP in complex with IACS-054647
Map dataPost-processed (sharpened, filtered) cryo-EM map
Sample
  • Complex: CDK11-cyclin L-SAP30BP bound by IACS-054647
    • Protein or peptide: SAP30-binding protein
    • Protein or peptide: Isoform 7 of Cyclin-dependent kinase 11B
    • Protein or peptide: Cyclin-L2
  • Ligand: 4-[8-[[(3~{S})-piperidin-3-yl]amino]imidazo[1,2-a]pyridin-6-yl]benzenecarbonitrile
KeywordsKinase / small molecule / splicing / transcription / inhibitor / TRANSFERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMcGeoch AJS / Greber BJ / Sheltzer JM
Funding support United Kingdom, 1 items
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 AJS / Greber BJ / Sheltzer JM
History
DepositionJun 30, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58734.png

Downloads & links

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Map

FileDownload / File: emd_58734.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed (sharpened, filtered) cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 224 pix.
= 224. Å		1 Å/pix.
x 224 pix.
= 224. Å		1 Å/pix.
x 224 pix.
= 224. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165
Minimum - Maximum-0.069247544 - 0.10273475
Average (Standard dev.)0.00000924322 (±0.002704379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 224.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58734_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map 1

Fileemd_58734_half_map_1.map
AnnotationUnfiltered half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map 2

Fileemd_58734_half_map_2.map
AnnotationUnfiltered half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CDK11-cyclin L-SAP30BP bound by IACS-054647

EntireName: CDK11-cyclin L-SAP30BP bound by IACS-054647
Components
  • Complex: CDK11-cyclin L-SAP30BP bound by IACS-054647
    • Protein or peptide: SAP30-binding protein
    • Protein or peptide: Isoform 7 of Cyclin-dependent kinase 11B
    • Protein or peptide: Cyclin-L2
  • Ligand: 4-[8-[[(3~{S})-piperidin-3-yl]amino]imidazo[1,2-a]pyridin-6-yl]benzenecarbonitrile

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Supramolecule #1: CDK11-cyclin L-SAP30BP bound by IACS-054647

SupramoleculeName: CDK11-cyclin L-SAP30BP bound by IACS-054647 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: SAP30-binding protein

MacromoleculeName: SAP30-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.186633 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMAGKKNV LSSLAVYAED SEPESDGEAG IEAVGSAAEE KGGLVSDAYG EDDFSRLGGD EDGYEEEEDE NSRQSEDDDS ETEKPEADD PKDNTEAEKR DPQELVASFS ERVRNMSPDE IKIPPEPPGR CSNHLQDKIQ KLYERKIKEG MDMNYIIQRK K EFRNPSIY ...String:
SNAMAGKKNV LSSLAVYAED SEPESDGEAG IEAVGSAAEE KGGLVSDAYG EDDFSRLGGD EDGYEEEEDE NSRQSEDDDS ETEKPEADD PKDNTEAEKR DPQELVASFS ERVRNMSPDE IKIPPEPPGR CSNHLQDKIQ KLYERKIKEG MDMNYIIQRK K EFRNPSIY EKLIQFCAID ELGTNYPKDM FDPHGWSEDS YYEALAKAQK IEMDKLEKAK KERTKIEFVT GTKKGTTTNA TS TTTTTAS TAVADAQKRK SKWDSAIPVT TIAQPTILTT TATLPAVVTV TTSASGSKTT VISAVGTIVK KAKQ

UniProtKB: SAP30-binding protein

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Macromolecule #2: Isoform 7 of Cyclin-dependent kinase 11B

MacromoleculeName: Isoform 7 of Cyclin-dependent kinase 11B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.970613 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMSEDEER ENENHLLVVP ESRFDRDSGE SEEAEEEVGE GTPQSSALTE GDYVPDSPAL SPIELKQELP KYLPALQGCR SVEEFQCLN RIEEGTYGVV YRAKDKKTDE IVALKRLKME KEKEGFPITS LREINTILKA QHPNIVTVRE IVVGSNMDKI Y IVMNYVEH ...String:
SNAMSEDEER ENENHLLVVP ESRFDRDSGE SEEAEEEVGE GTPQSSALTE GDYVPDSPAL SPIELKQELP KYLPALQGCR SVEEFQCLN RIEEGTYGVV YRAKDKKTDE IVALKRLKME KEKEGFPITS LREINTILKA QHPNIVTVRE IVVGSNMDKI Y IVMNYVEH DLKSLMETMK QPFLPGEVKT LMIQLLRGVK HLHDNWILHR DLKTSNLLLS HAGILKVGDF GLAREYGSPL KA Y(TPO)PVVVT LWYRAPELLL GAKEYSTAVD MWSVGCIFGE LLTQKPLFPG KSEIDQINKV FKDLGTPSEK IWPGYSELP AVKKMTFSEH PYNNLRKRFG ALLSDQGFDL MNKFLTYFPG RRISAEDGLK HEYFRETPLP IDPSMFPTWP AKSEQQRVKR GTSPRPPEG GLGYSQLGDD DLKETGFHLT TTNQGASAAG PGFSLKF

UniProtKB: Cyclin-dependent kinase 11B

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Macromolecule #3: Cyclin-L2

MacromoleculeName: Cyclin-L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.690453 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMAAAAAA AGAAGSAAPA AAAGAPGSGG APSGSQGVLI GDRLYSGVLI TLENCLLPDD KLRFTPSMSS GLDTDTETDL RVVGCELIQ AAGILLRLPQ VAMATGQVLF QRFFYTKSFV KHSMEHVSMA CVHLASKIEE APRRIRDVIN VFHRLRQLRD K KKPVPLLL ...String:
SNAMAAAAAA AGAAGSAAPA AAAGAPGSGG APSGSQGVLI GDRLYSGVLI TLENCLLPDD KLRFTPSMSS GLDTDTETDL RVVGCELIQ AAGILLRLPQ VAMATGQVLF QRFFYTKSFV KHSMEHVSMA CVHLASKIEE APRRIRDVIN VFHRLRQLRD K KKPVPLLL DQDYVNLKNQ IIKAERRVLK ELGFCVHVKH PHKIIVMYLQ VLECERNQHL VQTSWNYMND SLRTDVFVRF QP ESIACAC IYLAARTLEI PLPNRPHWFL LFGATEEEIQ EICLKILQLY ARKKVDLTHL EGEVEKRKHA IEEAKAQARG LLP GG

UniProtKB: Cyclin-L2

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Macromolecule #4: 4-[8-[[(3~{S})-piperidin-3-yl]amino]imidazo[1,2-a]pyridin-6-yl]be...

MacromoleculeName: 4-[8-[[(3~{S})-piperidin-3-yl]amino]imidazo[1,2-a]pyridin-6-yl]benzenecarbonitrile
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1KC9
Molecular weightTheoretical: 317.388 Da

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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

Concentration0.4 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
40.0 mMHEPES-KOH
200.0 mMPotassium chlorideKCl
2.0 mMMagnesium chlorideMgCl2
5.0 mMbeta-mercaptoethanol
25.0 uMIACS-054647
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec. / Details: Tergeo-EM plasma cleaner (PIE Scientific)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 5 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 12610 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber 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.
CTF correctionSoftware: (Name: cryoSPARC (ver. 5.0.6), RELION (ver. 5.0.1))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Initial map reconstructed during first structure determination of the complex (resulting in EMD-53224).
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.1) / Number images used: 363221
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 101300 / Software - Name: RELION (ver. 5.0.1)

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Atomic model buiding 1

Initial modelPDB ID:

9qkt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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