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- PDB-2jgz: Crystal structure of phospho-CDK2 in complex with Cyclin B -

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Basic information

Entry
Database: PDB / ID: 2jgz
TitleCrystal structure of phospho-CDK2 in complex with Cyclin B
Components
  • CELL DIVISION PROTEIN KINASE 2
  • G2/MITOTIC-SPECIFIC CYCLIN-B1
KeywordsTRANSFERASE / PROTEIN KINASE / UBL CONJUGATION / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE / KINASE / CYCLIN / MITOSIS / CELL CYCLE / ATP-BINDING / POLYMORPHISM / CELL DIVISION / NUCLEOTIDE-BINDING / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of chromosome condensation / Mitotic Prophase / E2F-enabled inhibition of pre-replication complex formation / G2/M DNA replication checkpoint / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / MASTL Facilitates Mitotic Progression ...response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of chromosome condensation / Mitotic Prophase / E2F-enabled inhibition of pre-replication complex formation / G2/M DNA replication checkpoint / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / MASTL Facilitates Mitotic Progression / positive regulation of mRNA 3'-end processing / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of attachment of spindle microtubules to kinetochore / Activation of NIMA Kinases NEK9, NEK6, NEK7 / patched binding / Phosphorylation of Emi1 / Transcriptional regulation by RUNX2 / tissue regeneration / Phosphorylation of the APC/C / Nuclear Pore Complex (NPC) Disassembly / outer kinetochore / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / cellular response to fatty acid / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / digestive tract development / oocyte maturation / cyclin-dependent protein serine/threonine kinase regulator activity / mitotic metaphase chromosome alignment / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / 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 / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / microtubule organizing center / ubiquitin-like protein ligase binding / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / positive regulation of G2/M transition of mitotic cell cycle / cyclin-dependent kinase / response to mechanical stimulus / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / positive regulation of cardiac muscle cell proliferation / cyclin-dependent protein kinase holoenzyme complex / Nuclear events stimulated by ALK signaling in cancer / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of mitotic cell cycle / post-translational protein modification / regulation of mitotic cell cycle / cyclin binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Resolution of Sister Chromatid Cohesion / positive regulation of DNA replication / Condensation of Prophase Chromosomes / mitotic spindle organization / meiotic cell cycle / male germ cell nucleus / cellular response to iron(III) ion / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / Orc1 removal from chromatin / spindle pole / Cyclin D associated events in G1
Similarity search - Function
: / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 ...: / : / 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
G2/mitotic-specific cyclin-B1 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBrown, N.R. / Petri, E. / Lowe, E.D. / Skamnaki, V. / Johnson, L.N.
CitationJournal: Cell Cycle / Year: 2007
Title: Cyclin B and cyclin A confer different substrate recognition properties on CDK2.
Authors: Brown, N.R. / Lowe, E.D. / Petri, E. / Skamnaki, V. / Antrobus, R. / Johnson, L.N.
History
DepositionFeb 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_status / struct_conn
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
B: G2/MITOTIC-SPECIFIC CYCLIN-B1


Theoretical massNumber of molelcules
Total (without water)63,1062
Polymers63,1062
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.780, 104.780, 251.635
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / P33 PROTEIN KINASE


Mass: 32999.125 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-288
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein G2/MITOTIC-SPECIFIC CYCLIN-B1 / CYCLIN B1


Mass: 30107.293 Da / Num. of mol.: 1 / Fragment: RESIDUES 167-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14635
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE SER 0 DERIVES FROM THE EXPRESSION CONSTRUCT A FRAGMENT CONTAINING RESIDUES 165-433 WAS USED ...RESIDUE SER 0 DERIVES FROM THE EXPRESSION CONSTRUCT A FRAGMENT CONTAINING RESIDUES 165-433 WAS USED IN THIS STUDY

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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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growpH: 6
Details: 0.9-1.2 M AMMONIUM SULPHATE, 100 MM MES PH 6.0-6.5, 100 MM POTASSIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→30.18 Å / Num. obs: 19123 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMZ

1qmz


Resolution: 2.9→29.64 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.864 / SU B: 15.137 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 2.771 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 979 5.2 %RANDOM
Rwork0.205 ---
obs0.208 17963 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 0 5 4437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9746144
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23423.819199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6315820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0711526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.22085
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23151
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6821.52807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22824457
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51431938
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5354.51687
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 74
Rwork0.272 1267

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