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- PDB-9fmr: Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835 -

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Basic information

Entry
Database: PDB / ID: 9fmr
TitleStructure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835
Components
  • Cyclin-K
  • Cyclin-dependent kinase 12
  • DNA damage-binding protein 1
KeywordsTRANSCRIPTION / Cyclin-dependent kinase / CDK / cyclin / inhibitor / SR-4835 / molecular glue
Function / homology
Function and homology information


cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / cyclin/CDK positive transcription elongation factor complex / negative regulation of intracellular estrogen receptor signaling pathway / host-mediated suppression of viral genome replication / regulation of MAP kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / cyclin/CDK positive transcription elongation factor complex / negative regulation of intracellular estrogen receptor signaling pathway / host-mediated suppression of viral genome replication / regulation of MAP kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / positive regulation by virus of viral protein levels in host cell / [RNA-polymerase]-subunit kinase / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / RNA polymerase II transcribes snRNA genes / regulation of cellular response to stress / cellular response to estrogen stimulus / regulation of signal transduction / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / viral release from host cell / cyclin-dependent kinase / cullin family protein binding / cyclin-dependent protein serine/threonine kinase activity / regulation of DNA-templated DNA replication initiation / Formation of HIV elongation complex in the absence of HIV Tat / positive regulation of viral genome replication / positive regulation of gluconeogenesis / RNA Polymerase II Transcription Elongation / negative regulation of MAPK cascade / Formation of RNA Pol II elongation complex / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA Polymerase II Pre-transcription Events / RNA splicing / regulation of embryonic development / cyclin binding / replication fork processing / TP53 Regulates Transcription of DNA Repair Genes / proteasomal protein catabolic process / positive regulation of transcription elongation by RNA polymerase II / epigenetic regulation of gene expression / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / nucleotide-excision repair / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / transcription by RNA polymerase II / cell population proliferation / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA processing / Formation of Incision Complex in GG-NER / positive regulation of protein catabolic process / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / regulation of cell population proliferation / rhythmic process / site of double-strand break / Neddylation / spermatogenesis / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein-macromolecule adaptor activity / protein kinase activity / chromosome, telomeric region / nuclear speck / protein ubiquitination / protein serine kinase activity / cell division / DNA repair / DNA damage response / nucleolus / protein kinase binding / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / : / extracellular exosome / nucleoplasm / ATP binding
Similarity search - Function
Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal ...Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / 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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-RMF / Cyclin-K / DNA damage-binding protein 1 / Cyclin-dependent kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsAnand, K. / Schmitz, M. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC2151-390873048 Germany
CitationJournal: Rsc Chem Biol / Year: 2024
Title: Discovery and design of molecular glue enhancers of CDK12-DDB1 interactions for targeted degradation of cyclin K.
Authors: Ghosh, P. / Schmitz, M. / Pandurangan, T. / Zeleke, S.T. / Chan, S.C. / Mosior, J. / Sun, L. / Palve, V. / Grassie, D. / Anand, K. / Frydman, S. / Roush, W.R. / Schonbrunn, E. / Geyer, M. / ...Authors: Ghosh, P. / Schmitz, M. / Pandurangan, T. / Zeleke, S.T. / Chan, S.C. / Mosior, J. / Sun, L. / Palve, V. / Grassie, D. / Anand, K. / Frydman, S. / Roush, W.R. / Schonbrunn, E. / Geyer, M. / Duckett, D. / Monastyrskyi, A.
History
DepositionJun 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Cyclin-dependent kinase 12
C: Cyclin-K
D: DNA damage-binding protein 1
E: Cyclin-dependent kinase 12
F: Cyclin-K
G: DNA damage-binding protein 1
H: Cyclin-dependent kinase 12
I: Cyclin-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,35712
Polymers505,8599
Non-polymers1,4983
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)249.521, 249.521, 218.535
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 1 through 393 or resid 709 through 1140))
d_2ens_1(chain "D" and (resid 1 through 393 or resid 709 through 1140))
d_3ens_1(chain "G" and (resid 1 through 393 or resid 709 through 1140))
d_1ens_2(chain "B" and (resid 713 through 1042 or resid 1101))
d_2ens_2chain "E"
d_3ens_2(chain "H" and (resid 713 through 1042 or resid 1101))
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETGLYGLYAA1 - 39329 - 421
d_12ens_1LYSLYSHISHISAA709 - 1140433 - 864
d_21ens_1METMETGLYGLYDD1 - 39329 - 421
d_22ens_1LYSLYSHISHISDD709 - 1140433 - 864
d_31ens_1METMETGLYGLYGG1 - 39329 - 421
d_32ens_1LYSLYSHISHISGG709 - 1140433 - 864
d_11ens_2GLYGLYLEULEUBB713 - 10421 - 330
d_12ens_2RMFRMFRMFRMFBJ1101
d_21ens_2GLYGLYLEULEUEE713 - 10421 - 330
d_22ens_2RMFRMFRMFRMFEK1101
d_31ens_2GLYGLYLEULEUHH713 - 10421 - 330
d_32ens_2RMFRMFRMFRMFHL1101
d_11ens_3THRTHRHISHISCC20 - 26721 - 268
d_21ens_3THRTHRHISHISFF20 - 26721 - 268
d_31ens_3THRTHRHISHISII20 - 26721 - 268

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.263654794853, 0.0784387244836, -0.961422651934), (-0.933367378307, -0.23089183551, -0.274798648846), (-0.243539496311, 0.969812521468, 0.0123364071043)-28.7274640373, -159.027846154, 72.7716982584
2given(0.173982162137, -0.950975126613, -0.255688317726), (0.096966481787, -0.241842268849, 0.965458346283), (-0.979963115973, -0.192765727144, 0.050136471464)-126.509150266, -103.11251078, -69.5605957804
3given(0.240467645527, 0.0768913483735, -0.967606858181), (-0.930069842117, -0.266995440154, -0.252355946476), (-0.277750607991, 0.960625398104, 0.00731055938159)-31.3825486835, -160.089219442, 68.7106570572
4given(0.207835779604, -0.945378055968, -0.25112670111), (0.120881873856, -0.22994126674, 0.965667948325), (-0.970665679464, -0.231057017085, 0.0664890484719)-122.847284318, -100.202923608, -70.7191397051
5given(0.224166388363, 0.0538267704044, -0.973063260593), (-0.923088549566, -0.30844477243, -0.229715807076), (-0.312501135979, 0.949718116679, -0.0194560752246)-35.3520446883, -162.292640481, 63.6779863583
6given(0.271462105811, -0.935597636419, -0.225755150189), (0.103306191548, -0.204883117863, 0.97331944335), (-0.956888789723, -0.287541250506, 0.0410350260197)-114.885037122, -100.427184685, -74.0140624915

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Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 96425.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: human DDB1 (1-1140, delta396-705 replaced with GNGNSE) with an N-terminal HisSpy-tag as described for AddGene plasmid #124213.,human DDB1 (1-1140, delta396-705 replaced with GNGNSE) with an ...Details: human DDB1 (1-1140, delta396-705 replaced with GNGNSE) with an N-terminal HisSpy-tag as described for AddGene plasmid #124213.,human DDB1 (1-1140, delta396-705 replaced with GNGNSE) with an N-terminal HisSpy-tag as described for AddGene plasmid #124213.,human DDB1 (1-1140, delta396-705 replaced with GNGNSE) with an N-terminal HisSpy-tag as described for AddGene plasmid #124213.,human DDB1 (1-1140, delta396-705 replaced with GNGNSE) with an N-terminal HisSpy-tag as described for AddGene plasmid #124213.
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein Cyclin-dependent kinase 12 / Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 ...Cdc2-related kinase / arginine/serine-rich / CrkRS / Cell division cycle 2-related protein kinase 7 / CDC2-related protein kinase 7 / Cell division protein kinase 12 / hCDK12


Mass: 40764.992 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: our construct starts at GQTES...ends at PPPS we have added the compound named RMF into it. it is not replacing any residue, it is a compound name that is already recognized by pdb (pl. see pdb 8p81 or 8bu5)
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK12, CRK7, CRKRS, KIAA0904 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#3: Protein Cyclin-K


Mass: 31429.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK, CPR4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75909
#4: Chemical ChemComp-RMF / ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine


Mass: 499.356 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C21H20Cl2N10O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: 1 M potassium citrate and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 1401478 / % possible obs: 91.42 % / Redundancy: 19.6 % / Biso Wilson estimate: 210.19 Å2 / CC1/2: 0.997 / Net I/σ(I): 5.9
Reflection shellResolution: 3.9→4.04 Å / Num. unique obs: 1811 / CC1/2: 0.117

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→36.71 Å / SU ML: 0.6285 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.1091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2498 3785 3.07 %
Rwork0.2078 119560 -
obs0.2091 123345 89.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 243.17 Å2
Refinement stepCycle: LAST / Resolution: 3.9→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33778 0 102 5 33885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002334601
X-RAY DIFFRACTIONf_angle_d0.543546788
X-RAY DIFFRACTIONf_chiral_restr0.04215176
X-RAY DIFFRACTIONf_plane_restr0.00335995
X-RAY DIFFRACTIONf_dihedral_angle_d11.520612937
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.17693578033
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.15368503224
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.34729276458
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS1.47315332673
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.908610697273
ens_3d_3CCX-RAY DIFFRACTIONTorsion NCS0.685736558513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.950.319930.4216148X-RAY DIFFRACTION2.98
3.95-40.5078200.4111709X-RAY DIFFRACTION14.16
4-4.060.3901590.38252025X-RAY DIFFRACTION41.06
4.06-4.110.36771170.38113325X-RAY DIFFRACTION66.85
4.11-4.180.3171390.37434176X-RAY DIFFRACTION84.99
4.18-4.240.43511440.36394838X-RAY DIFFRACTION96.68
4.24-4.310.36151540.34384985X-RAY DIFFRACTION99.38
4.31-4.380.40221530.34074928X-RAY DIFFRACTION99.76
4.38-4.460.35951620.32144965X-RAY DIFFRACTION99.96
4.46-4.550.3321520.30765031X-RAY DIFFRACTION100
4.55-4.640.29931520.29794906X-RAY DIFFRACTION99.96
4.64-4.740.29511580.2855051X-RAY DIFFRACTION100
4.74-4.850.32481560.27424904X-RAY DIFFRACTION99.98
4.85-4.970.29641560.25585010X-RAY DIFFRACTION100
4.97-5.110.32751600.24744964X-RAY DIFFRACTION99.98
5.11-5.260.30041560.25334938X-RAY DIFFRACTION100
5.26-5.430.26921660.24234991X-RAY DIFFRACTION99.98
5.43-5.620.28971580.24374988X-RAY DIFFRACTION100
5.62-5.840.2361560.23414948X-RAY DIFFRACTION100
5.85-6.110.25871560.22494940X-RAY DIFFRACTION100
6.11-6.430.26611660.22545008X-RAY DIFFRACTION100
6.43-6.830.30761600.22744959X-RAY DIFFRACTION100
6.83-7.350.24411510.2014986X-RAY DIFFRACTION100
7.35-8.090.24251640.18574991X-RAY DIFFRACTION100
8.09-9.240.17351500.1574959X-RAY DIFFRACTION100
9.24-11.580.14811680.11354934X-RAY DIFFRACTION99.69
11.59-36.710.24471490.15794953X-RAY DIFFRACTION99.18
Refinement TLS params.Method: refined / Origin x: -77.8352352448 Å / Origin y: -72.4046882779 Å / Origin z: 22.6262540869 Å
111213212223313233
T1.82286197503 Å20.130385304727 Å20.126348213281 Å2-1.99365055812 Å2-0.146527602034 Å2--1.78116614665 Å2
L0.407886079275 °2-0.155718694352 °20.160015021346 °2-0.324047603289 °2-0.137576160937 °2--0.22905295312 °2
S-0.0132427242582 Å °-0.166755993166 Å °0.00299932018365 Å °0.0321384771743 Å °0.0389565631258 Å °0.0400933408194 Å °-0.068408134502 Å °-0.0827627692826 Å °-0.023369879693 Å °
Refinement TLS groupSelection details: all

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