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- PDB-6ath: Cdk2/cyclin A/p27-KID-deltaC -

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Basic information

Entry
Database: PDB / ID: 6ath
TitleCdk2/cyclin A/p27-KID-deltaC
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
  • Cyclin-dependent kinase inhibitor 1B
KeywordsTRANSFERASE / Inhibitor / Complex / IDP / CDK / Cyclin / kinase / Phosphortlation
Function / homology
Function and homology information


cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of phosphorylation / negative regulation of epithelial cell proliferation involved in prostate gland development / : ...cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of phosphorylation / negative regulation of epithelial cell proliferation involved in prostate gland development / : / cyclin A2-CDK1 complex / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / cell cycle G1/S phase transition / regulation of exit from mitosis / negative regulation of epithelial cell apoptotic process / epithelial cell proliferation involved in prostate gland development / ubiquitin ligase activator activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to leptin stimulus / RHO GTPases activate CIT / male pronucleus / female pronucleus / nuclear export / response to glucagon / cellular response to cocaine / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to antibiotic / cyclin-dependent protein serine/threonine kinase regulator activity / Cul4A-RING E3 ubiquitin ligase complex / molecular function inhibitor activity / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / cellular response to lithium ion / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cochlea development / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity / G2 Phase / 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 / protein kinase inhibitor activity / X chromosome / PTK6 Regulates Cell Cycle / Constitutive Signaling by AKT1 E17K in Cancer / 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) / microtubule organizing center / : / inner ear development / centriole replication / regulation of G1/S transition of mitotic cell cycle / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / regulation of DNA replication / centrosome duplication / negative regulation of mitotic cell cycle / Telomere Extension By Telomerase / G0 and Early G1 / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / response to amino acid / Activation of the pre-replicative complex / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / response to glucose / 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 / response to cadmium ion / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / cellular response to platelet-derived growth factor stimulus / Notch signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of microtubule polymerization / FLT3 Signaling / Hsp70 protein binding / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / male germ cell nucleus / regulation of cell migration / positive regulation of DNA replication
Similarity search - Function
Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin ...Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclin-A2 / Cyclin-dependent kinase 2 / Cyclin-dependent kinase inhibitor 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWhite, S.W. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA82491, P30 CA21765 United States
CitationJournal: Nat Commun / Year: 2019
Title: Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation.
Authors: Tsytlonok, M. / Sanabria, H. / Wang, Y. / Felekyan, S. / Hemmen, K. / Phillips, A.H. / Yun, M.K. / Waddell, M.B. / Park, C.G. / Vaithiyalingam, S. / Iconaru, L. / White, S.W. / Tompa, P. / ...Authors: Tsytlonok, M. / Sanabria, H. / Wang, Y. / Felekyan, S. / Hemmen, K. / Phillips, A.H. / Yun, M.K. / Waddell, M.B. / Park, C.G. / Vaithiyalingam, S. / Iconaru, L. / White, S.W. / Tompa, P. / Seidel, C.A.M. / Kriwacki, R.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Cyclin-A2
C: Cyclin-dependent kinase inhibitor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5454
Polymers72,4493
Non-polymers961
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-54 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.191, 77.645, 137.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34200.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 30142.834 Da / Num. of mol.: 1 / Fragment: UNP residues 173-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P20248
#3: Protein Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinase inhibitor p27 / p27Kip1


Mass: 8105.980 Da / Num. of mol.: 1 / Fragment: UNP residues 22-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDKN1B, KIP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P46527
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: HEPES, Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 71452 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.6
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6848 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPv9.2.10phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JSU

1jsu


Resolution: 1.82→29.625 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.44
RfactorNum. reflection% reflection
Rfree0.1873 3582 5.02 %
Rwork0.1711 --
obs0.1719 71378 98.61 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 42.912 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--0.1949 Å20 Å2-0 Å2
2--1.6979 Å2-0 Å2
3----1.503 Å2
Refinement stepCycle: LAST / Resolution: 1.82→29.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 5 399 5160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054903
X-RAY DIFFRACTIONf_angle_d0.946661
X-RAY DIFFRACTIONf_dihedral_angle_d14.0821830
X-RAY DIFFRACTIONf_chiral_restr0.068746
X-RAY DIFFRACTIONf_plane_restr0.005840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8158-1.83970.27721200.29142071X-RAY DIFFRACTION80
1.8397-1.86490.28921470.25962484X-RAY DIFFRACTION96
1.8649-1.89150.23991210.22862560X-RAY DIFFRACTION98
1.8915-1.91970.22251520.2172509X-RAY DIFFRACTION97
1.9197-1.94970.25811510.19152533X-RAY DIFFRACTION97
1.9497-1.98170.22141390.17872541X-RAY DIFFRACTION98
1.9817-2.01580.20511390.16212579X-RAY DIFFRACTION100
2.0158-2.05250.18361380.15732652X-RAY DIFFRACTION100
2.0525-2.0920.17721390.15462587X-RAY DIFFRACTION100
2.092-2.13460.17791350.15312603X-RAY DIFFRACTION100
2.1346-2.1810.16791700.14842629X-RAY DIFFRACTION100
2.181-2.23180.16681240.15312618X-RAY DIFFRACTION100
2.2318-2.28760.17491320.15862641X-RAY DIFFRACTION100
2.2876-2.34940.19381290.16132610X-RAY DIFFRACTION100
2.3494-2.41850.19161280.16092662X-RAY DIFFRACTION100
2.4185-2.49650.16661350.1612644X-RAY DIFFRACTION100
2.4965-2.58570.23781110.16152638X-RAY DIFFRACTION100
2.5857-2.68910.17811450.16832663X-RAY DIFFRACTION100
2.6891-2.81140.17221460.16982623X-RAY DIFFRACTION100
2.8114-2.95950.1771190.18082670X-RAY DIFFRACTION100
2.9595-3.14480.21121310.18272684X-RAY DIFFRACTION100
3.1448-3.38730.19031460.17722657X-RAY DIFFRACTION100
3.3873-3.72750.17661440.15852681X-RAY DIFFRACTION100
3.7275-4.26560.15251480.15092681X-RAY DIFFRACTION100
4.2656-5.36890.1691460.15812728X-RAY DIFFRACTION100
5.3689-29.62860.20111470.20012848X-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)
11.2434-0.4186-0.17760.95920.40751.1998-0.0896-0.14580.01120.11930.00570.0630.2019-0.05120.03140.0761-0.01950.03790.1253-0.03490.096317.19389.272171.8809
20.98570.1627-0.20981.41350.37421.1638-0.04010.02050.0272-0.0243-0.00160.07530.1071-0.0280.02540.08610.00180.01390.0636-0.01540.070831.8965-5.551445.743
30.1466-0.1567-0.09790.1956-0.0711.4249-0.2282-0.3142-0.56080.78550.03520.1470.4297-0.025-0.17440.9315-0.07110.1370.23070.17620.260723.0649-23.980267.163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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