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- PDB-3g33: Crystal structure of CDK4/cyclin D3 -

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Basic information

Entry
Database: PDB / ID: 3g33
TitleCrystal structure of CDK4/cyclin D3
Components
  • CCND3 protein
  • Cell division protein kinase 4
KeywordsCELL CYCLE / Ser/Thr protein kinase / phosphorylation / ATP-binding / Cell division / Disease mutation / Kinase / Nucleotide-binding / Phosphoprotein / Proto-oncogene / Serine/threonine-protein kinase / Transferase / Cyclin
Function / homology
Function and homology information


cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / regulation of transcription initiation by RNA polymerase II / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 ...cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / regulation of transcription initiation by RNA polymerase II / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / regulation of type B pancreatic cell proliferation / regulation of insulin receptor signaling pathway / Transcriptional regulation by RUNX2 / cellular response to phorbol 13-acetate 12-myristate / mitotic cell cycle phase transition / cyclin-dependent protein serine/threonine kinase activator activity / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase regulator activity / PTK6 Regulates Cell Cycle / regulation of cyclin-dependent protein serine/threonine kinase activity / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / positive regulation of cyclin-dependent protein serine/threonine kinase activity / bicellular tight junction / cyclin-dependent protein kinase holoenzyme complex / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / T cell proliferation / positive regulation of G2/M transition of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cellular response to interleukin-4 / cyclin binding / response to organic substance / Ubiquitin-dependent degradation of Cyclin D / G1/S transition of mitotic cell cycle / MAPK6/MAPK4 signaling / Oncogene Induced Senescence / RMTs methylate histone arginines / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / positive regulation of fibroblast proliferation / regulation of cell population proliferation / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / nuclear membrane / cellular response to lipopolysaccharide / transcription regulator complex / nuclear body / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of protein phosphorylation / cell division / protein phosphorylation / protein serine kinase activity / host cell nucleus / positive regulation of cell population proliferation / chromatin / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin D / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal ...Cyclin D / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cyclin-dependent kinase 4 / G1/S-specific cyclin-D3 / G1/S-specific cyclin-D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTakaki, T. / Echalier, A. / Brown, N.R. / Hunt, T. / Endicott, J.A. / Noble, M.E.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The structure of CDK4/cyclin D3 has implications for models of CDK activation.
Authors: Takaki, T. / Echalier, A. / Brown, N.R. / Hunt, T. / Endicott, J.A. / Noble, M.E.
History
DepositionFeb 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 4
B: CCND3 protein
C: Cell division protein kinase 4
D: CCND3 protein


Theoretical massNumber of molelcules
Total (without water)136,4814
Polymers136,4814
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-35 kcal/mol
Surface area47220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.297, 141.297, 143.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Cell division protein kinase 4 / / Cyclin-dependent kinase 4 / PSK-J3


Mass: 34184.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11802, cyclin-dependent kinase
#2: Protein CCND3 protein / Cyclin D3 / isoform CRA_b


Mass: 34056.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCND3, hCG_16683 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6FG62, UniProt: P30281*PLUS

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1 M Hepes, 15% PEG 3,350, 10% tacsimate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Nov 17, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3→57.83 Å / Num. obs: 29147 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 105 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.039 / Net I/σ(I): 13.8
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4033 / % possible all: 94.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.19 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.888 / SU B: 66.121 / SU ML: 0.524 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31442 1481 5.1 %RANDOM
Rwork0.2814 ---
obs0.28304 27629 98 %-
all-27629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 3→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8158 0 0 0 8158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0228338
X-RAY DIFFRACTIONr_angle_refined_deg0.5351.9811308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.19251033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.66822.652362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.552151417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7491578
X-RAY DIFFRACTIONr_chiral_restr0.040.21273
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216288
X-RAY DIFFRACTIONr_mcbond_it0.0861.55187
X-RAY DIFFRACTIONr_mcangle_it0.16428358
X-RAY DIFFRACTIONr_scbond_it0.19333151
X-RAY DIFFRACTIONr_scangle_it0.3664.52950
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 105 -
Rwork0.383 1874 -
obs--92 %
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)
14.8369-1.3441-0.1466.9305-0.63973.27630.38810.75941.3832-0.8861-0.145-0.3146-1.0026-0.1431-0.24310.8573-0.01740.16331.18880.28220.8488-36.075-11.789-57.33
29.13670.4989-2.23954.4302-2.76647.719-0.1136-0.8110.37920.2510.04-0.1256-0.0790.34340.07350.01760.02310.00720.85550.04920.52528.515-34.051-36.031
35.25570.9590.38395.88032.25415.6216-0.07460.606-1.1003-0.74160.2123-0.13720.51240.1497-0.13780.4651-0.03340.06411.05760.11920.84825.346-48.484-65.01
46.9099-0.08661.00793.58870.76579.69250.0502-0.4965-0.1712-0.0493-0.0770.05670.44480.13520.02690.05020.00110.05670.78220.12360.4456-20.249-37.721-36.81
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 300
2X-RAY DIFFRACTION2B23 - 254
3X-RAY DIFFRACTION3C10 - 300
4X-RAY DIFFRACTION4D23 - 254

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