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- PDB-6gu6: CDK1/Cks2 in complex with Dinaciclib -

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Basic information

Entry
Database: PDB / ID: 6gu6
TitleCDK1/Cks2 in complex with Dinaciclib
Components
  • Cyclin-dependent kinase 1
  • Cyclin-dependent kinases regulatory subunit 2
KeywordsCELL CYCLE / CDK1 / CKS2 / INHIBITOR
Function / homology
Function and homology information


regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint ...regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / MASTL Facilitates Mitotic Progression / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / meiosis I / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / protein localization to kinetochore / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / response to copper ion / chromosome condensation / centrosome cycle / [RNA-polymerase]-subunit kinase / SCF ubiquitin ligase complex / G1/S-Specific Transcription / cyclin-dependent protein kinase activity / MAPK3 (ERK1) activation / response to amine / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / regulation of embryonic development / cellular response to organic cyclic compound / response to axon injury / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / Cyclin A/B1/B2 associated events during G2/M transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle cell proliferation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / epithelial cell differentiation / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / AURKA Activation by TPX2 / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / ubiquitin binding / response to activity / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / peptidyl-threonine phosphorylation / MAPK6/MAPK4 signaling / PKR-mediated signaling / spindle microtubule / regulation of circadian rhythm / response to toxic substance / mitotic spindle / positive regulation of protein import into nucleus / microtubule cytoskeleton organization / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / Ovarian tumor domain proteases / rhythmic process / Regulation of TP53 Degradation / cell migration / kinase activity / virus receptor activity / midbody / histone binding / fibroblast proliferation / protein-containing complex assembly / peptidyl-serine phosphorylation / response to ethanol
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / 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
Chem-1QK / Cyclin-dependent kinases regulatory subunit / Cyclin-dependent kinase 1 / Cyclin-dependent kinases regulatory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWood, D.J. / Korolchuk, S. / Tatum, N.J. / Wang, L.Z. / Endicott, J.A. / Noble, M.E.M. / Martin, M.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N009738/1 United Kingdom
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2019
Title: Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition.
Authors: Wood, D.J. / Korolchuk, S. / Tatum, N.J. / Wang, L.Z. / Endicott, J.A. / Noble, M.E.M. / Martin, M.P.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 1
B: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2423
Polymers44,8452
Non-polymers3971
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-7 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.704, 97.232, 108.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cyclin-dependent kinase 1 / CDK1 / Cell division control protein 2 homolog / Cell division protein kinase 1 / p34 protein kinase


Mass: 34553.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Plasmid: pVL1393 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-dependent kinases regulatory subunit 2 / CKS-2


Mass: 10290.819 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P33552, UniProt: K9J4F7*PLUS
#3: Chemical ChemComp-1QK / 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium / DINACICLIB


Mass: 397.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.33→72.43 Å / Num. obs: 21580 / % possible obs: 99.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YC6

4yc6


Resolution: 2.33→72.43 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24586 1077 5 %RANDOM
Rwork0.20092 ---
obs0.20317 20503 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.498 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å2-0 Å2
2---1.73 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.33→72.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 29 86 3058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193051
X-RAY DIFFRACTIONr_bond_other_d00.022865
X-RAY DIFFRACTIONr_angle_refined_deg1.851.974128
X-RAY DIFFRACTIONr_angle_other_deg3.5982.9866656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6355355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20823.475141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41515547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.61520
X-RAY DIFFRACTIONr_chiral_restr0.1170.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213314
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02626
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0484.4411429
X-RAY DIFFRACTIONr_mcbond_other4.0494.4381428
X-RAY DIFFRACTIONr_mcangle_it6.1036.6481781
X-RAY DIFFRACTIONr_mcangle_other6.1016.6511782
X-RAY DIFFRACTIONr_scbond_it4.9055.021621
X-RAY DIFFRACTIONr_scbond_other4.9055.0211621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6057.2932348
X-RAY DIFFRACTIONr_long_range_B_refined9.97551.13452
X-RAY DIFFRACTIONr_long_range_B_other9.9851.13444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.327→2.388 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 67 -
Rwork0.278 1450 -
obs--96.99 %

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