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- PDB-1h25: CDK2/Cyclin A in complex with an 11-residue recruitment peptide f... -

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Basic information

Entry
Database: PDB / ID: 1h25
TitleCDK2/Cyclin A in complex with an 11-residue recruitment peptide from retinoblastoma-associated protein
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
  • RETINOBLASTOMA-ASSOCIATED PROTEIN
KeywordsTRANSFERASE / CELL CYCLE / PROTEIN KINASE / CYCLIN / CDK2 / RECRUITMENT / PEPTIDE SPECIFICITY
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / importin-alpha family protein binding / positive regulation of transcription regulatory region DNA binding / : / cyclin A2-CDK1 complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of extracellular matrix organization / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of centromere complex assembly / cellular response to luteinizing hormone stimulus / positive regulation of macrophage differentiation / cell cycle G1/S phase transition / glial cell apoptotic process / tissue homeostasis / protein localization to chromosome, centromeric region / positive regulation of mitotic metaphase/anaphase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / negative regulation of hepatocyte apoptotic process / neuron maturation / male pronucleus / female pronucleus / myoblast differentiation / digestive tract development / aortic valve morphogenesis / Replication of the SARS-CoV-1 genome / response to glucagon / cellular response to cocaine / SWI/SNF complex / negative regulation of cold-induced thermogenesis / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of glial cell proliferation / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / negative regulation of G1/S transition of mitotic cell cycle / cyclin E1-CDK2 complex / hepatocyte apoptotic process / 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 / X chromosome / PTK6 Regulates Cell Cycle / RUNX2 regulates osteoblast differentiation / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / skeletal muscle cell differentiation / microtubule organizing center / centriole replication / 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 apoptotic signaling pathway / negative regulation of cell cycle / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / chromosome organization / chondrocyte differentiation / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / 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 / Nuclear events stimulated by ALK signaling in cancer / 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 / mitotic G1 DNA damage checkpoint signaling / striated muscle cell differentiation / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle
Similarity search - Function
Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) ...Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / 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 / : / 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
Retinoblastoma-associated protein / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTews, I. / Cheng, K.Y. / Lowe, E.D. / Noble, M.E.M. / Brown, N.R. / Gul, S. / Gamblin, S. / Johnson, L.N.
Citation
Journal: Biochemistry / Year: 2002
Title: Specificity Determinants of Recruitment Peptides Bound to Phospho-Cdk2/Cyclin A
Authors: Lowe, E.D. / Tews, I. / Cheng, K.Y. / Brown, N.R. / Gul, S. / Noble, M.E.M. / Gamblin, S. / Johnson, L.N.
#1: Journal: Nat.Cell Biol. / Year: 1999
Title: The Structural Basis for Specificity of Substrate and Recruitment Peptides for Cyclin-Dependant Kinases
Authors: Brown, N.R. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N.
History
DepositionJul 31, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
E: RETINOBLASTOMA-ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)129,7855
Polymers129,7855
Non-polymers00
Water3,459192
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: RETINOBLASTOMA-ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)65,5643
Polymers65,5643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2


Theoretical massNumber of molelcules
Total (without water)64,2212
Polymers64,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.609, 133.851, 147.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.01024, -0.46678, 0.88432), (-0.50805, -0.76414, -0.39746), (0.86127, -0.44521, -0.24497)8.39902, 142.11066, 69.97775
2given(0.02746, -0.48661, 0.87319), (-0.48015, -0.77257, -0.41543), (0.87675, -0.40786, -0.25486)10.06276, 143.19574, 68.52282
DetailsBIOMOLECULE 1 IS A TRIMERIC COMPLEX OF CHAINS A, B AND E. BIOMOLECULE 2 IS A DIMERIC COMPLEX OF CHAINS C AND D

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / CYCLIN-DEPENDENT KINASE 2 / P33 PROTEIN KINASE


Mass: 34467.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein CYCLIN A2 / CYCLIN A


Mass: 29753.410 Da / Num. of mol.: 2 / Fragment: CYCLIN FOLD, RESIDUES 175-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20248
#3: Protein/peptide RETINOBLASTOMA-ASSOCIATED PROTEIN / PP110 / P105-RB / RB


Mass: 1342.670 Da / Num. of mol.: 1 / Fragment: RESIDUES 869-878 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P06400
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCDK2: CONTROL OF THE CELL CYCLE DURING S PHASE AND G2. BELONGS TO THE SER/THR FAMILY OF PROTEIN ...CDK2: CONTROL OF THE CELL CYCLE DURING S PHASE AND G2. BELONGS TO THE SER/THR FAMILY OF PROTEIN KINASES. CYCLIN A2: CONTROL OF THE CELL CYCLE. INTERACTS WITH THE CDK2 AND CDC2 PROTEIN KINASES. RETINOBLASTOMA-ASSOCIATED PROTEIN: TRANSCRIPTION ACTIVATOR INVOLVED IN CELL CYCLE REGULATION AND DNA REPLICATION.
Has protein modificationY
Sequence detailsCHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING OF RESIDUES 175-432

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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: 3.1 Å3/Da / Density % sol: 59.8 %
Crystal growpH: 7
Details: 0.8M KCL, 1.2M (NH4)2SO4, 40MM HEPES PH 7.0. PROTEIN CONCENTRATION = 10MG/ML
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMHEPES1droppH7.4
3150 mM1dropNaCl
43.4 mMEDTA1drop
50.01 %azide1drop
60.01 %monothiglycerol1drop
70.8 M1reservoirKCl
81.2 Mammonium sulfate1reservoir
9100 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→28.99 Å / Num. obs: 52141 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.7 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 252831
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMZ

1qmz


Resolution: 2.5→28 Å / SU B: 11.694 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2627 5.1 %RANDOM
Rwork0.249 ---
obs0.249 48967 99.9 %-
Displacement parametersBiso mean: 55.509 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20 Å2
2--1.82 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8845 0 0 192 9037
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.38
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.56 Å / Rfactor Rfree: 0.361 / Rfactor Rwork: 0.338 / Num. reflection Rwork: 194 / Total num. of bins used: 20

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