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- PDB-2w99: Crystal Structure of CDK4 in complex with a D-type cyclin -

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Basic information

Entry
Database: PDB / ID: 2w99
TitleCrystal Structure of CDK4 in complex with a D-type cyclin
Components
  • CELL DIVISION PROTEIN KINASE 4
  • G1/S-SPECIFIC CYCLIN-D1
KeywordsCELL CYCLE / SERINE/THREONINE-PROTEIN KINASE / CHROMOSOMAL REARRANGEMENT / ATP-BINDING / TRANSFERASE / POLYMORPHISM / CELL DIVISION / PROTO-ONCOGENE / PHOSPHOPROTEIN / DISEASE MUTATION / NUCLEOTIDE-BINDING / CYCLIN DEPENDENT KINASE / KINASE / CYCLIN / ONCOLOGY / DRUG DESGN
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 / cyclin D1-CDK6 complex / 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 / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of transcription initiation by RNA polymerase II ...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 / cyclin D1-CDK6 complex / 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 / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of transcription initiation by RNA polymerase II / Leydig cell differentiation / RUNX3 regulates WNT signaling / response to leptin / Transcriptional regulation by RUNX2 / proline-rich region binding / cyclin-dependent protein serine/threonine kinase activator activity / response to iron ion / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase regulator activity / response to UV-A / response to X-ray / response to vitamin E / response to corticosterone / PTK6 Regulates Cell Cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / animal organ regeneration / Transcriptional Regulation by VENTX / bicellular tight junction / RUNX3 regulates p14-ARF / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / cyclin-dependent kinase / transcription repressor complex / cyclin-dependent protein serine/threonine kinase activity / response to magnesium ion / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / cyclin-dependent protein kinase holoenzyme complex / mitotic G1 DNA damage checkpoint signaling / liver development / positive regulation of fibroblast proliferation / protein serine/threonine kinase activator activity / cyclin binding / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Ubiquitin-dependent degradation of Cyclin D / Transcriptional regulation of white adipocyte differentiation / response to calcium ion / response to estrogen / Oncogene Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / histone deacetylase binding / Transcriptional regulation of granulopoiesis / SCF(Skp2)-mediated degradation of p27/p21 / SPOP-mediated proteasomal degradation of PD-L1(CD274) / RMTs methylate histone arginines / regulation of gene expression / Cyclin D associated events in G1 / transcription corepressor activity / response to estradiol / nuclear membrane / transcription regulator complex / Interleukin-4 and Interleukin-13 signaling / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / response to ethanol / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / positive regulation of cell population proliferation / DNA damage response / nucleolus / protein kinase binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-D1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDay, P.J. / Cleasby, A. / Tickle, I.J. / Reilly, M.O. / Coyle, J.E. / Holding, F.P. / McMenamin, R.L. / Yon, J. / Chopra, R. / Lengauer, C. / Jhoti, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal Structure of Human Cdk4 in Complex with a D-Type Cyclin.
Authors: Day, P.J. / Cleasby, A. / Tickle, I.J. / O'Reilly, M. / Coyle, J.E. / Holding, F.P. / Mcmenamin, R.L. / Yon, J. / Chopra, R. / Lengauer, C. / Jhoti, H.
History
DepositionJan 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G1/S-SPECIFIC CYCLIN-D1
B: CELL DIVISION PROTEIN KINASE 4


Theoretical massNumber of molelcules
Total (without water)65,5352
Polymers65,5352
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-11.9 kcal/mol
Surface area30860 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.023, 64.684, 188.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein G1/S-SPECIFIC CYCLIN-D1 / D-TYPE CYCLIN / PRAD1 ONCOGENE


Mass: 30990.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24385
#2: Protein CELL DIVISION PROTEIN KINASE 4 / CDK4 / CYCLIN-DEPENDENT KINASE 4 / PSK-J3


Mass: 34544.625 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-44,48-303 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P11802, cyclin-dependent kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, GLY 43 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLY 44 TO GLU ...ENGINEERED RESIDUE IN CHAIN B, GLY 43 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLY 44 TO GLU ENGINEERED RESIDUE IN CHAIN B, THR 172 TO ALA
Sequence detailsRESIDUES 1-271 WERE EXPRESSED, BUT THE N AND C-TERMINAL WERE DISORDERED AND THEREFORE NOT COMPLETE ...RESIDUES 1-271 WERE EXPRESSED, BUT THE N AND C-TERMINAL WERE DISORDERED AND THEREFORE NOT COMPLETE IN THE MODEL. HIS TAG WAS ADDED AT THE C-TERMINAL. RESIDUES 45, 46, 47 IN CHAIN B WERE DELETED.

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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: 2.84 Å3/Da / Density % sol: 56.28 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.8→94.5 Å / Num. obs: 17640 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 78.76 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / % possible all: 94.8

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Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BLX

1blx


Resolution: 2.8→94.49 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY WHERE THE DENSITY WAS NOT CLEAR. IN REGIONS WHERE THE DENSITY WAS UNINTERPRETABLE OR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY WHERE THE DENSITY WAS NOT CLEAR. IN REGIONS WHERE THE DENSITY WAS UNINTERPRETABLE OR ABSENT, RESIDUES WERE OMITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 845 4.79 %RANDOM
Rwork0.213 ---
obs0.216 17640 98.3 %-
Displacement parametersBiso mean: 86.21 Å2
Baniso -1Baniso -2Baniso -3
1--4.53183 Å20 Å20 Å2
2--10.1525 Å20 Å2
3----5.62067 Å2
Refinement stepCycle: LAST / Resolution: 2.8→94.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 0 126 4385
LS refinement shellResolution: 2.8→2.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2633 132 4.97 %
Rwork0.2142 2524 -
all0.2166 2656 -
obs--98.27 %

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