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- PDB-4yc6: CDK1/CKS1 -

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Basic information

Entry
Database: PDB / ID: 4yc6
TitleCDK1/CKS1
Components
  • Cyclin-dependent kinase 1
  • Cyclin-dependent kinases regulatory subunit 1
KeywordsCELL CYCLE / CDK1 / Cyclin B1 / CKS2
Function / homology
Function and homology information


regulation of Schwann cell differentiation / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / ventricular cardiac muscle cell development / histone kinase activity / Golgi disassembly ...regulation of Schwann cell differentiation / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / ventricular cardiac muscle cell development / histone kinase activity / Golgi disassembly / E2F-enabled inhibition of pre-replication complex formation / microtubule cytoskeleton organization involved in mitosis / Depolymerization of the Nuclear Lamina / MASTL Facilitates Mitotic Progression / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Phosphorylation of Emi1 / Transcriptional regulation by RUNX2 / mitotic nuclear membrane disassembly / Nuclear Pore Complex (NPC) Disassembly / Phosphorylation of the APC/C / G2/M DNA replication checkpoint / protein localization to kinetochore / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase / chromosome condensation / Condensation of Prometaphase Chromosomes / response to amine / centrosome cycle / positive regulation of ubiquitin-dependent protein catabolic process / response to copper ion / SCF ubiquitin ligase complex / cyclin-dependent protein kinase activity / regulation of heterochromatin organization / peptidyl-threonine phosphorylation / MAPK3 (ERK1) activation / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / positive regulation of cardiac muscle cell proliferation / Regulation of APC/C activators between G1/S and early anaphase / ERK1 and ERK2 cascade / response to axon injury / response to cadmium ion / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein deubiquitination / positive regulation of G2/M transition of mitotic cell cycle / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / epithelial cell differentiation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / RNA polymerase II CTD heptapeptide repeat kinase activity / negative regulation of protein ubiquitination / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / regulation of embryonic development / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / AURKA Activation by TPX2 / cyclin binding / positive regulation of DNA replication / response to activity / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / spindle microtubule / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / ubiquitin binding / positive regulation of protein import into nucleus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / positive regulation of protein localization to nucleus / microtubule cytoskeleton organization / PKR-mediated signaling / response to toxic substance / mitotic spindle / MAPK6/MAPK4 signaling / cellular response to hydrogen peroxide / regulation of circadian rhythm / SCF(Skp2)-mediated degradation of p27/p21 / kinase activity / Cyclin D associated events in G1 / The role of GTSE1 in G2/M progression after G2 checkpoint / Ovarian tumor domain proteases / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / rhythmic process / cell migration / virus receptor activity / protein-containing complex assembly / midbody / histone binding / response to ethanol / DNA replication
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 / : / Phosphorylase Kinase; 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 / : / 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 1 / Cyclin-dependent kinases regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsBrown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W. / Moukhametzianov, R. / Noble, M.E.M. / Endicott, J.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0901526 United Kingdom
Cancer Research UKC240/A15751 United Kingdom
Astex PharmaceuticalsNICR-Alliance United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: CDK1 structures reveal conserved and unique features of the essential cell cycle CDK.
Authors: Brown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W.A. / Moukhametzianov, R. / Noble, M.E. / Endicott, J.A.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 1
B: Cyclin-dependent kinases regulatory subunit 1
C: Cyclin-dependent kinase 1
D: Cyclin-dependent kinases regulatory subunit 1
E: Cyclin-dependent kinase 1
F: Cyclin-dependent kinases regulatory subunit 1
G: Cyclin-dependent kinase 1
H: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)178,6028
Polymers178,6028
Non-polymers00
Water11,512639
1
A: Cyclin-dependent kinase 1
B: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6 kcal/mol
Surface area18210 Å2
MethodPISA
2
C: Cyclin-dependent kinase 1
D: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-6 kcal/mol
Surface area18180 Å2
MethodPISA
3
E: Cyclin-dependent kinase 1
F: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area18170 Å2
MethodPISA
4
G: Cyclin-dependent kinase 1
H: Cyclin-dependent kinases regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)44,6512
Polymers44,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.817, 147.531, 87.297
Angle α, β, γ (deg.)90.000, 92.060, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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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: 34142.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / 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 1 / CKS-1


Mass: 10508.093 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1B, CKS1, PNAS-143, PNAS-16 / Production host: Escherichia coli (E. coli) / References: UniProt: P61024
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.3 / Details: 16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4 / PH range: 8.2-8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→75.09 Å / Num. all: 50462 / Num. obs: 50462 / % possible obs: 97 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.094 / Rsym value: 0.084 / Net I/σ(I): 16.6
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 3.7 % / Rmerge(I) obs: 2.08 / Mean I/σ(I) obs: 1.97 / % possible all: 80.6

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
REFMAC5.8.0103refinement
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.6→75.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1787 3.5 %RANDOM
Rwork0.2248 48643 --
obs0.2268 50430 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.11 Å2 / Biso mean: 95.396 Å2 / Biso min: 39.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-2.01 Å2
2--4.54 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→75.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11632 0 0 639 12271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911998
X-RAY DIFFRACTIONr_bond_other_d00.0211516
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9716234
X-RAY DIFFRACTIONr_angle_other_deg3.625326586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0551418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94323.83564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.959152168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7581572
X-RAY DIFFRACTIONr_chiral_restr0.1080.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113234
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022734
X-RAY DIFFRACTIONr_mcbond_it2.2963.2455702
X-RAY DIFFRACTIONr_mcbond_other2.2933.2445701
X-RAY DIFFRACTIONr_mcangle_it3.9434.8437110
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.391 3068 -
obs--79.71 %
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)
17.11431.8715-0.867.3283-0.30916.23930.29660.59510.0656-0.1403-0.05870.8259-0.0012-0.2544-0.23790.33560.09190.00310.0852-0.08670.66-30.47820.323-8.335
27.47591.25931.96058.4019-0.38077.1468-0.06540.3388-0.212-0.251-0.2116-0.7360.0990.2930.2770.31580.0330.03910.03420.0570.50191.0267.154-6.925
38.7432-2.12251.5173.914-1.01618.1139-0.5183-1.01751.0106-0.03050.14640.95610.0344-0.8990.3720.9955-0.1209-0.21940.2549-0.33771.4835-31.21211.779-37.256
47.93320.2738-2.96449.35060.48247.7061-0.5512-0.4404-0.3769-0.02440.4193-0.6783-0.25550.67190.13180.8674-0.1540.23740.1083-0.04510.48863.16110.173-35.953
53.3471-0.7259-0.97614.89511.99351.9985-0.51060.06990.0055-1.90450.27540.8446-0.9919-0.04150.23511.8946-0.2148-0.30320.07270.15490.7128-16.31634.791-43.65
65.6995-1.4623.18062.8678-1.63929.9060.27010.9214-0.4019-0.9453-0.328-0.26860.36620.78210.05780.79650.0650.11460.1603-0.06790.80239.78634.961-21.55
74.61191.1687-1.04314.7014-0.6081.50020.2198-0.48670.35470.5691-0.24370.0959-0.34790.09280.02390.6513-0.01020.04730.0719-0.11270.3965-6.9135.136-0.077
86.2846-1.0554-2.42460.98982.82368.3134-0.20831.01480.295-0.1197-0.21510.1155-0.0458-0.66130.42350.7187-0.1461-0.00680.394-0.02910.8816-39.132-9.704-16.837
95.96710.5212-0.56363.9647-0.17091.20690.0589-0.0841-0.06930.4888-0.19240.13680.1715-0.20630.13340.6154-0.04550.04580.05760.00950.3335-22.508-5.4764.34
105.6917-2.0101-5.53871.7213-0.439711.4434-0.35-0.65720.3437-0.0680.1345-0.21170.9980.63250.21551.2505-0.1204-0.05730.2427-0.17740.8434-1.904-18.366-21.834
114.5911-0.1962.52885.39260.313.56650.1360.0971-0.0384-1.0008-0.01680.48510.6956-0.1129-0.11921.2465-0.259-0.02580.0742-0.06760.4541-15.603-11.613-44.33
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 73
2X-RAY DIFFRACTION2D5 - 73
3X-RAY DIFFRACTION3F5 - 73
4X-RAY DIFFRACTION4H5 - 73
5X-RAY DIFFRACTION5G1 - 290
6X-RAY DIFFRACTION6A1 - 80
7X-RAY DIFFRACTION7A81 - 289
8X-RAY DIFFRACTION8C1 - 80
9X-RAY DIFFRACTION9C81 - 289
10X-RAY DIFFRACTION10E1 - 80
11X-RAY DIFFRACTION11E81 - 289

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