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- PDB-5uq1: Crystal structure of human Cdk2-Spy1 complex -

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Basic information

Entry
Database: PDB / ID: 5uq1
TitleCrystal structure of human Cdk2-Spy1 complex
Components
  • Cyclin-dependent kinase 2
  • Speedy protein A
KeywordsTRANSFERASE/CELL CYCLE / phosphotransferase / protein kinase / cell cycle regulation / TRANSFERASE-CELL CYCLE complex
Function / homology
Function and homology information


meiotic attachment of telomere to nuclear envelope / establishment of protein localization to telomere / male meiotic nuclear division / XY body / telomere capping / oogenesis / protein kinase activator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex ...meiotic attachment of telomere to nuclear envelope / establishment of protein localization to telomere / male meiotic nuclear division / XY body / telomere capping / oogenesis / protein kinase activator activity / 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 / cyclin-dependent protein kinase activity / Y chromosome / 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 / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / positive regulation of protein kinase activity / Cajal body / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / response to organic substance / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / regulation of gene expression / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / DNA damage response / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cell cycle regulatory protein Speedy / Cell cycle regulatory protein / 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 ...Cell cycle regulatory protein Speedy / Cell cycle regulatory protein / 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 2 / Speedy protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsMcGrath, D.A. / Tripathi, S.M. / Rubin, S.M.
CitationJournal: EMBO J. / Year: 2017
Title: Structural basis of divergent cyclin-dependent kinase activation by Spy1/RINGO proteins.
Authors: McGrath, D.A. / Fifield, B.A. / Marceau, A.H. / Tripathi, S. / Porter, L.A. / Rubin, S.M.
History
DepositionFeb 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Speedy protein A
C: Cyclin-dependent kinase 2
D: Speedy protein A


Theoretical massNumber of molelcules
Total (without water)107,2444
Polymers107,2444
Non-polymers00
Water0
1
A: Cyclin-dependent kinase 2
B: Speedy protein A


Theoretical massNumber of molelcules
Total (without water)53,6222
Polymers53,6222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-6 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: Cyclin-dependent kinase 2
D: Speedy protein A


Theoretical massNumber of molelcules
Total (without water)53,6222
Polymers53,6222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.359, 75.359, 325.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cyclin-dependent kinase 2 / / Cell division protein kinase 2 / p33 protein kinase


Mass: 34309.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Speedy protein A / Rapid inducer of G2/M progression in oocytes A / hSpy/Ringo A / Speedy-1 / Spy1


Mass: 19312.221 Da / Num. of mol.: 2 / Fragment: UNP residues 61-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPDYA, SPDY1, SPY1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MJ70

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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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 1M lithium chloride, 12% PEG 6000, and 0.1M MES pH 6.2, harvested and flash frozen in the same solution with 20% PEG 200.

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→46.111 Å / Num. obs: 17634 / % possible obs: 94.7 % / Redundancy: 6.2 % / CC1/2: 0.98 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8971 / CC1/2: 0.62 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.201→46.111 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 865 4.91 %
Rwork0.2051 --
obs0.2079 17621 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.201→46.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 0 0 6913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067095
X-RAY DIFFRACTIONf_angle_d1.0499618
X-RAY DIFFRACTIONf_dihedral_angle_d14.2412604
X-RAY DIFFRACTIONf_chiral_restr0.0441070
X-RAY DIFFRACTIONf_plane_restr0.0061213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2005-3.4010.3881940.30152333X-RAY DIFFRACTION80
3.401-3.66350.34821400.24972506X-RAY DIFFRACTION87
3.6635-4.0320.28091470.2142896X-RAY DIFFRACTION100
4.032-4.6150.23391750.17652915X-RAY DIFFRACTION100
4.615-5.81250.25211520.19352967X-RAY DIFFRACTION100
5.8125-46.11550.21781570.18713139X-RAY DIFFRACTION99
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)
10.0092-0.00160.00770.01010.00810.0103-0.0722-0.0937-0.0820.1274-0.099-0.0824-0.1241-0.0264-0.00090.5690.0010.03370.2858-0.00470.330725.47553.540619.1117
20.04780.0297-00.0213-0.01410.0191-0.10530.1904-0.015-0.12460.0830.00220.0393-0.0385-0.2040.1993-0.2867-0.135-0.037-0.10730.05779.23383.846118.3202
30.00620.00490.00330.16930.08020.04190.0428-0.0438-0.11480.2098-0.0458-0.08750.0535-0.00450.09520.2366-0.21420.02610.1747-0.02140.114510.39487.601735.3124
40.0338-0.0246-0.00760.0344-0.02360.04180.1142-0.11110.22070.1304-0.02820.3524-0.139-0.04650.10040.2732-0.25230.07750.0727-0.02270.2855-2.731716.265630.8527
50.02730.0022-0.01450.0229-0.01730.0201-0.08130.0623-0.0669-0.0592-0.01370.0610.1119-0.0463-0.00090.5969-0.1865-0.04030.66320.1380.609225.6062-22.64145.9649
60.0021-0.0023-0.00040.0008-0.00130.0014-0.02220.020.0408-0.03870.02630.06-0.0237-0.0565-00.2879-0.082-0.06190.4264-0.01370.238327.2598-6.352452.3803
70.06160.02530.10640.01620.05450.19530.1742-0.0389-0.1963-0.00590.1487-0.022-0.0042-0.09190.04010.287-0.11910.00620.19470.13080.389926.3249-13.050139.4039
80.0456-0.0419-0.05640.0750.08070.10140.0675-0.2306-0.0478-0.14660.1549-0.00590.09330.03440.02460.2979-0.122-0.00570.44890.05040.397125.8692-7.162741.2381
90.25220.13750.07550.15090.03150.1329-0.22420.13210.13820.0424-0.00680.02050.0767-0.0042-0.44170.415-0.2093-0.02110.04610.01760.222119.962334.2415.5398
100.00220.0009-0.00140.0015-0.0011-0-0.02240.0502-0.0549-0.0022-0.0154-0.03310.0212-0.0058-00.5688-0.10980.05080.51030.06210.346931.723427.971331.5471
110.0559-0.03760.0290.04240.00260.02640.11390.0620.15150.01-0.1781-0.34630.09290.06880.00030.3554-0.0336-0.00460.35250.0060.435941.815122.616424.091
120.0297-0.0426-0.04930.06090.07010.07910.0246-0.00760.07470.03850.01570.0035-0.0883-0.0211-0.00590.6904-0.2579-0.120.37020.09460.708123.064865.255528.46
130.0307-0.00530.00090.03780.02510.02390.0289-0.03780.02890.2070.033-0.02820.0894-0.0635-0.02050.39-0.1390.01580.2040.03970.384317.332756.392539.4702
140.1493-0.07290.00420.0772-0.06870.14190.0578-0.055-0.12280.0370.04360.0679-0.02260.00760.17630.33-0.23130.08550.09530.06570.173510.841445.08838.254
150.01150.0056-0.02010.04320.00610.0365-0.09090.0506-0.01770.0275-0.05450.0357-0.05650.0152-0.02020.4032-0.18060.01750.3525-0.01040.306223.905953.058826.7431
160.00340.0012-0.00260.0003-0.00320.0027-0.01490.01620.03920.0682-0.0092-0.06760.06330.06630.00010.5379-0.17730.08870.47760.04630.467328.027357.768242.0928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 296 )
5X-RAY DIFFRACTION5chain 'B' and (resid 67 through 80 )
6X-RAY DIFFRACTION6chain 'B' and (resid 81 through 97 )
7X-RAY DIFFRACTION7chain 'B' and (resid 98 through 134 )
8X-RAY DIFFRACTION8chain 'B' and (resid 135 through 200 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 158 )
10X-RAY DIFFRACTION10chain 'C' and (resid 159 through 181 )
11X-RAY DIFFRACTION11chain 'C' and (resid 182 through 289 )
12X-RAY DIFFRACTION12chain 'D' and (resid 63 through 71 )
13X-RAY DIFFRACTION13chain 'D' and (resid 72 through 119 )
14X-RAY DIFFRACTION14chain 'D' and (resid 120 through 170 )
15X-RAY DIFFRACTION15chain 'D' and (resid 171 through 185 )
16X-RAY DIFFRACTION16chain 'D' and (resid 186 through 201 )

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