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- PDB-9bjc: Crystal structure of CDK2/Cyclin E1 in complex with XC208 -

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Basic information

Entry
Database: PDB / ID: 9bjc
TitleCrystal structure of CDK2/Cyclin E1 in complex with XC208
Components
  • Cyclin-dependent kinase 2
  • G1/S-specific cyclin-E1
KeywordsCELL CYCLE / TRANSFERASE/INHIBITOR / Cyclin-dependent kinase 2 G1/S-specific Cyclin-E1 Inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity ...positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity / G2 Phase / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / G1/S-Specific Transcription / regulation of anaphase-promoting complex-dependent catabolic process / Association of TriC/CCT with target proteins during biosynthesis / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / DNA replication initiation / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / telomere maintenance / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / CDK-mediated phosphorylation and removal of Cdc6 / G1/S transition of mitotic cell cycle / SCF(Skp2)-mediated degradation of p27/p21 / peptidyl-serine phosphorylation / DNA Damage/Telomere Stress Induced Senescence / Orc1 removal from chromatin / potassium ion transport / Meiotic recombination / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / Regulation of TP53 Degradation / cellular senescence / kinase activity / nuclear envelope / Processing of DNA double-strand break ends / regulation of protein localization / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / DNA replication / protein phosphorylation / endosome / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA-templated transcription / centrosome / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / 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, 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
: / G1/S-specific cyclin-E1 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsHosford, C.J. / Yano, J. / Thevakumaran, N. / Davison, J. / Romeril, S. / Choi, Y. / Hadjithomas, M. / Verdine, G.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Nature-guided discovery of a tunable kinase inhibitor scaffold
Authors: Verdine, G.L.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: G1/S-specific cyclin-E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4873
Polymers67,1402
Non-polymers3471
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-22 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.332, 76.332, 258.708
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34143.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein G1/S-specific cyclin-E1


Mass: 32996.449 Da / Num. of mol.: 1 / Fragment: residues 96-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNE1, CCNE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P24864
#3: Chemical ChemComp-A1AQZ / (5aS,6S,7S)-3,7-dihydroxy-6-methoxy-1,4,6,9-tetramethyl-6,7-dihydrodibenzo[b,f][1,4]oxazepine-8,11(5aH,10H)-dione / XC208


Mass: 347.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 3.6M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.22→43.14 Å / Num. obs: 44428 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.986 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.068 / Rrim(I) all: 0.227 / Χ2: 0.98 / Net I/σ(I): 6.8
Reflection shellResolution: 2.22→2.28 Å / Redundancy: 10.9 % / Rmerge(I) obs: 2.775 / Num. unique obs: 3221 / CC1/2: 0.414 / Rpim(I) all: 0.87 / Rrim(I) all: 2.911 / Χ2: 1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→43.12 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 2300 5.19 %
Rwork0.194 --
obs0.195 44309 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 25 192 4859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084787
X-RAY DIFFRACTIONf_angle_d0.8956507
X-RAY DIFFRACTIONf_dihedral_angle_d7.383623
X-RAY DIFFRACTIONf_chiral_restr0.051730
X-RAY DIFFRACTIONf_plane_restr0.007816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.270.34811290.3142529X-RAY DIFFRACTION98
2.27-2.320.34421540.29622586X-RAY DIFFRACTION100
2.32-2.380.32931370.27912586X-RAY DIFFRACTION100
2.38-2.440.26631380.25832565X-RAY DIFFRACTION100
2.44-2.510.2831370.24162578X-RAY DIFFRACTION100
2.51-2.60.24071360.23822615X-RAY DIFFRACTION100
2.6-2.690.27051440.23532583X-RAY DIFFRACTION100
2.69-2.80.25771100.23742646X-RAY DIFFRACTION100
2.8-2.920.24551620.2262605X-RAY DIFFRACTION100
2.92-3.080.26591310.21122623X-RAY DIFFRACTION100
3.08-3.270.24371280.21562619X-RAY DIFFRACTION100
3.27-3.520.25451400.19272635X-RAY DIFFRACTION100
3.52-3.880.21461360.17162677X-RAY DIFFRACTION100
3.88-4.440.16671740.15242651X-RAY DIFFRACTION100
4.44-5.590.16291580.16072679X-RAY DIFFRACTION100
5.59-43.120.17321860.16822832X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.48112.72312.3666.3632-0.616.70060.102-0.4275-0.26031.36760.4041.09870.4253-0.94-0.80490.93540.1081-0.24680.76270.02921.019612.9707-3.66427.4247
20.7608-1.10661.31946.9454-1.33982.4718-0.04030.00310.3966-0.60030.31120.8896-0.0195-0.2971-0.23050.31270.0093-0.10290.43970.10260.493221.1663-7.070130.0192
33.4851-1.4458-0.70644.09081.16562.36890.56931.5129-0.2668-1.436-0.70930.167-0.2854-0.54050.02240.92120.1825-0.09481.1094-0.09720.364728.4601-23.744810.4926
45.4236-2.916-2.13083.248-0.34373.99470.3171.22230.5623-0.4691-0.5866-0.5672-0.3245-0.09290.17790.7409-0.04220.01330.89420.16740.833448.3405-16.38525.8251
53.129-0.4531-0.27073.13040.36172.1551-0.119-0.27820.25320.25580.14880.0051-0.1774-0.048-0.02120.23350.0367-0.01920.3858-0.01830.350831.3596-18.676449.1706
67.7685-5.3753-2.37624.25841.55951.65260.39270.65560.363-0.3212-0.534-0.4269-0.27630.03750.1010.2968-0.0067-0.01840.39730.0350.440442.2216-19.821335.6712
73.661-3.98080.85874.5996-0.38851.48670.52941.8549-0.1629-1.3938-0.39710.04010.42470.55870.20290.60430.03070.0890.8381-0.0240.519548.6582-33.265725.0623
84.4818-1.24780.20543.28930.23122.6214-0.063-0.29310.18260.16640.0532-0.6748-0.09280.27950.03930.1880.0127-0.06210.3652-0.01280.413251.9132-26.58344.5258
94.91060.50651.49576.41552.83292.9725-0.0009-0.2772-0.41590.5230.304-0.4736-0.01440.6497-0.36540.27940.0250.00370.60670.05970.426744.0637-30.958651.1226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 296 )
4X-RAY DIFFRACTION4chain 'B' and (resid 101 through 126 )
5X-RAY DIFFRACTION5chain 'B' and (resid 127 through 236 )
6X-RAY DIFFRACTION6chain 'B' and (resid 237 through 257 )
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 271 )
8X-RAY DIFFRACTION8chain 'B' and (resid 272 through 353 )
9X-RAY DIFFRACTION9chain 'B' and (resid 354 through 377 )

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