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- PDB-5uq3: Crystal structure of human Cdk2-Spy1-P27 ternary complex -

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Basic information

Entry
Database: PDB / ID: 5uq3
TitleCrystal structure of human Cdk2-Spy1-P27 ternary complex
Components
  • Cyclin-dependent kinase 2
  • Cyclin-dependent kinase inhibitor 1B
  • Speedy protein A
KeywordsTransferase/Transferase Inhibitor / phosphotransferase / protein kinase / cell cycle regulation / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / meiotic attachment of telomere to nuclear envelope / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / establishment of protein localization to telomere / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / male meiotic nuclear division ...cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / meiotic attachment of telomere to nuclear envelope / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / establishment of protein localization to telomere / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / male meiotic nuclear division / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / epithelial cell proliferation involved in prostate gland development / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of phosphorylation / ubiquitin ligase activator activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / XY body / telomere capping / RHO GTPases activate CIT / nuclear export / AKT phosphorylates targets in the cytosol / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / cellular response to antibiotic / negative regulation of kinase activity / oogenesis / cellular response to lithium ion / molecular function inhibitor activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / protein kinase inhibitor activity / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / protein kinase activator activity / 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 cyclin-dependent protein serine/threonine kinase activity / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / regulation of anaphase-promoting complex-dependent catabolic process / negative regulation of vascular associated smooth muscle cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / inner ear development / centrosome duplication / Telomere Extension By Telomerase / cellular response to organic cyclic compound / G0 and Early G1 / negative regulation of mitotic cell cycle / Activation of the pre-replicative complex / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / positive regulation of protein kinase activity / response to amino acid / cyclin-dependent kinase / localization / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cajal body / response to glucose / Activation of ATR in response to replication stress / response to cadmium ion / 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 / positive regulation of microtubule polymerization / regulation of cell migration / Notch signaling pathway / mitotic G1 DNA damage checkpoint signaling / Hsp70 protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / FLT3 Signaling / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / placenta development / sensory perception of sound / potassium ion transport / G1/S transition of mitotic cell cycle / negative regulation of cell growth / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21
Similarity search - Function
Cell cycle regulatory protein Speedy / Cell cycle regulatory protein / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Cell cycle regulatory protein Speedy / Cell cycle regulatory protein / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / 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 / Cyclin-dependent kinase inhibitor 1B / Speedy protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Speedy protein A
C: Cyclin-dependent kinase inhibitor 1B


Theoretical massNumber of molelcules
Total (without water)76,0643
Polymers76,0643
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-24 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.650, 124.650, 88.490
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.: 1
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.: 1 / 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
#3: Protein Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinase inhibitor p27 / p27Kip1


Mass: 22441.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDKN1B, KIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46527

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 5% PEG 6000, 0.1M MES pH 5.0

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→68.44 Å / Num. obs: 9501 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.5
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 7 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2 / Num. unique obs: 2220 / CC1/2: 0.68 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→53.975 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.02
RfactorNum. reflection% reflection
Rfree0.3237 953 10.09 %
Rwork0.243 --
obs0.2512 9448 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→53.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 0 0 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043783
X-RAY DIFFRACTIONf_angle_d1.0225132
X-RAY DIFFRACTIONf_dihedral_angle_d15.531388
X-RAY DIFFRACTIONf_chiral_restr0.041557
X-RAY DIFFRACTIONf_plane_restr0.007654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6002-3.78990.42741350.33081186X-RAY DIFFRACTION100
3.7899-4.02730.35171310.29991218X-RAY DIFFRACTION99
4.0273-4.33810.41081290.26571176X-RAY DIFFRACTION100
4.3381-4.77450.31831380.22611202X-RAY DIFFRACTION100
4.7745-5.46480.31241350.24721212X-RAY DIFFRACTION100
5.4648-6.88280.33181390.27951223X-RAY DIFFRACTION100
6.8828-53.98110.27241460.1911278X-RAY DIFFRACTION100
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)
10.08150.2520.29980.2419-0.79710.7096-0.1526-0.16031.3778-1.29320.22590.2215-0.77271.68440.08440.13070.8839-0.3814-1.14320.84941.119931.126834.20215.5265
20.5250.1781-0.1870.1525-0.07320.0584-0.43760.1365-0.5511-0.37930.23980.549-0.3106-0.8362-0.18670.72080.01450.16420.45310.08370.675340.748123.818811.3182
30.00840.24010.03310.03210.0858-0.0273-0.22790.0868-0.0056-0.3790.0234-0.8229-0.3955-0.54710.02741.19420.13640.07840.40170.06890.632133.69532.193116.9392
40.03590.0071-0.0508-0.00880.05520.07440.6939-0.5127-0.1878-0.0384-0.0627-0.1609-0.0837-0.48180.00870.63880.1433-0.03430.72180.05950.964117.798718.8778-0.772
50.23570.0041-0.32370.1739-0.23360.45570.16370.39160.4866-1.0423-0.19860.71560.37140.3640.00270.65750.03130.02650.69630.17160.466734.022318.97292.1043
60.02760.15790.32020.26720.00070.0013-0.5312-0.3567-1.36671.28731.5507-1.29151.06380.90040.02151.05170.18920.2870.87120.19720.362739.53688.313214.0692
70.00320.01380.0374-0.0172-0.04080.04180.2170.55670.0009-0.0871-0.30910.33480.6204-0.69710.00121.00450.2059-0.01460.76730.19750.863637.58070.823911.06
80.4211-0.07720.0330.59210.04590.0583-1.266-0.5104-0.08720.69841.09460.76691.8985-0.1239-0.04391.5140.59560.2591-1.86790.32490.653527.77760.91053.4754
90.0858-0.1605-0.14220.0590.21470.0679-0.1560.0365-0.1108-0.2752-0.04020.48470.43480.4128-0.00022.17160.1502-0.1891.394-0.05810.858830.4162-10.78186.4113
100.49520.1549-0.01640.26360.15410.02670.55911.3651-0.3627-0.8794-0.52550.77650.74940.7860.65890.74540.21450.08050.66760.02910.475332.70067.0927-8.4722
110.2065-0.16960.05730.07880.10620.0822-0.13690.07210.8110.7516-0.2438-1.2118-0.79950.7798-0.0406-0.4266-0.8997-0.50621.0391-0.16860.680867.240422.272325.901
120.11230.03290.0740.09850.12240.1338-0.11910.36820.2050.4727-0.0838-0.22220.1384-0.3820.02050.8897-0.46920.09010.6841-0.58611.220559.796310.936536.3969
130.6053-0.7288-0.00610.20520.0430.69390.52241.0526-0.18380.50390.6636-0.56460.0680.33130.06950.6392-0.0777-0.12690.1397-0.08340.520653.486417.401827.4358
140.409-0.0097-0.24160.2138-0.26380.2865-0.0793-0.0725-0.36620.40390.30170.22340.0462-1.1040.01551.75720.18660.06821.0911-0.03460.618544.981317.7942.4422
150.62340.4009-0.74380.8243-0.6181.17831.04721.01331.79271.25250.7862-0.3216-0.8371-0.55660.12730.7138-0.0881-0.10420.9049-0.07850.830147.440626.524225.3411
160.10790.1022-0.0940.32360.17770.24390.4815-0.2728-0.2472-1.1870.2139-0.8447-0.12560.91430.01190.79270.26640.03671.1503-0.19081.02864.686114.871816.5935
170.23930.1972-0.10590.503-0.14980.00240.2190.04260.18320.44220.10850.1256-0.4247-0.12150.03610.95350.0833-0.68260.9273-0.07050.937660.5126.1921.8859
18-0.00610.01660.02680.0005-0.01170.0279-0.277-0.34950.32870.26040.4510.47670.101-0.05220.00111.56640.1422-0.01711.191-0.36410.862340.661342.359619.7505
190.6042-0.0063-0.35320.4749-0.00040.1412-0.5453-0.1234-0.58140.4032-0.61820.5124-0.5428-0.1753-0.09641.60590.21-0.23640.7924-0.04951.489830.021142.471922.2009
200.1122-0.03410.03620.0142-0.02760.0716-0.1739-0.1343-0.1391-0.3798-0.3193-0.09030.4953-0.17470.00211.03510.0930.11730.92190.13422.20830.278746.405811.675
210.5565-0.06030.77410.2607-0.24831.2941.2561-0.4829-0.13-0.29060.88460.63070.4831-1.55660.54470.69820.26220.74951.09330.41681.784122.626731.430113.7704
220.08730.06910.01750.0797-0.05790.1780.78330.098-0.25660.18770.2524-0.6543-0.3974-0.21760.00351.2771-0.1369-0.40771.4926-0.2991.105729.463116.947222.3249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 100 )
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 168 )
7X-RAY DIFFRACTION7chain 'A' and (resid 169 through 181 )
8X-RAY DIFFRACTION8chain 'A' and (resid 182 through 229 )
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 247 )
10X-RAY DIFFRACTION10chain 'A' and (resid 248 through 292 )
11X-RAY DIFFRACTION11chain 'B' and (resid 67 through 80 )
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 89 )
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 147 )
14X-RAY DIFFRACTION14chain 'B' and (resid 148 through 157 )
15X-RAY DIFFRACTION15chain 'B' and (resid 158 through 178 )
16X-RAY DIFFRACTION16chain 'B' and (resid 179 through 193 )
17X-RAY DIFFRACTION17chain 'B' and (resid 194 through 201 )
18X-RAY DIFFRACTION18chain 'C' and (resid 557 through 566 )
19X-RAY DIFFRACTION19chain 'C' and (resid 567 through 576 )
20X-RAY DIFFRACTION20chain 'C' and (resid 577 through 581 )
21X-RAY DIFFRACTION21chain 'C' and (resid 582 through 595 )
22X-RAY DIFFRACTION22chain 'C' and (resid 596 through 602 )

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