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- PDB-1h24: CDK2/CyclinA in complex with a 9 residue recruitment peptide from E2F -

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Basic information

Entry
Database: PDB / ID: 1h24
TitleCDK2/CyclinA in complex with a 9 residue recruitment peptide from E2F
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
  • TRANSCRIPTION FACTOR E2F1
KeywordsTRANSFERASE / CELL CYCLE / PROTEIN KINASE / CYCLIN / CDK2 / RECRUITMENT / PEPTIDE SPECIFICITY / SERINE/THREONINE-PROTEIN KINASE / ATP- BINDING / CELL DIVISION / MITOSIS / PHOSPHORYLATION
Function / homology
Function and homology information


Rb-E2F complex / lens fiber cell apoptotic process / negative regulation of fat cell proliferation / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by DREAM complex ...Rb-E2F complex / lens fiber cell apoptotic process / negative regulation of fat cell proliferation / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by DREAM complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / mRNA stabilization / cellular response to leptin stimulus / male pronucleus / female pronucleus / Activation of NOXA and translocation to mitochondria / anoikis / response to glucagon / cellular response to cocaine / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / Activation of PUMA and translocation to mitochondria / negative regulation of fat cell differentiation / positive regulation of DNA biosynthetic process / DNA-binding transcription activator activity / G1/S-Specific Transcription / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / 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 / negative regulation of DNA binding / PTK6 Regulates Cell Cycle / Transcriptional Regulation by E2F6 / regulation of G1/S transition of mitotic cell cycle / regulation of anaphase-promoting complex-dependent catabolic process / regulation of DNA replication / 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 / intrinsic apoptotic signaling pathway by p53 class mediator / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / animal organ regeneration / cyclin-dependent kinase / cis-regulatory region sequence-specific DNA binding / cyclin-dependent protein serine/threonine kinase activity / Activation of ATR in response to replication stress / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / forebrain development / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / DNA damage checkpoint signaling / male germ cell nucleus / response to organic substance / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / Oncogene Induced Senescence / 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 / Pre-NOTCH Transcription and Translation / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / Cyclin D associated events in G1 / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of fibroblast proliferation / G2/M transition of mitotic cell cycle / cellular senescence / cellular response to xenobiotic stimulus / Regulation of TP53 Degradation / sequence-specific double-stranded DNA binding / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends
Similarity search - Function
E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : ...E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding 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 / Winged helix DNA-binding domain superfamily / 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. / Winged helix-like DNA-binding domain superfamily / 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-A2 / Cyclin-dependent kinase 2 / Transcription factor E2F1
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

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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: TRANSCRIPTION FACTOR E2F1


Theoretical massNumber of molelcules
Total (without water)129,5715
Polymers129,5715
Non-polymers00
Water4,161231
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: TRANSCRIPTION FACTOR E2F1


Theoretical massNumber of molelcules
Total (without water)65,3503
Polymers65,3503
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)73.551, 133.549, 147.890
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(0.00672, -0.45653, 0.088968), (-0.49064, -0.77676, -0.39487), (0.87134, -0.43386, -0.22921)7.86501, 142.55656, 68.35345
2given(0.01666, -0.47452, 0.88009), (-0.46663, -0.78216, -0.41289), (0.8843, -0.4038, -0.23445)9.22201, 143.5574, 66.8957
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
Details: PHOSPHORYLATED ON THR160 / 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 FRAGMENT, 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 TRANSCRIPTION FACTOR E2F1 / E2F-1 / PRB-BINDING PROTEIN E2F-1 / PBR3 / RETINOBLASTOMA-ASSOCIATED PROTEIN 1 / RBAP-1


Mass: 1128.345 Da / Num. of mol.: 1 / Fragment: RESIDUES 87-95 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q01094
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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. E2F: TRANSCRIPTION ACTIVATOR INVOLVED IN CELL CYCLE REGULATION DNA REPLICATION.
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 Å3/Da / Density % sol: 59 %
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→28.8 Å / Num. obs: 48503 / % possible obs: 95.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.7 / % possible all: 94.4
Reflection
*PLUS
Num. measured all: 124102
Reflection shell
*PLUS
% possible obs: 94.4 %

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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→28.8 Å / SU B: 14.242 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.313
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2474 5.1 %RANDOM
Rwork0.209 ---
obs0.212 45989 94.67 %-
Displacement parametersBiso mean: 55.703 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--1.03 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8970 0 0 231 9201
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.85
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.56 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.264 / Num. reflection Rwork: 173 / Total num. of bins used: 20

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