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- PDB-1gy3: pCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate -

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Basic information

Entry
Database: PDB / ID: 1gy3
TitlepCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
  • SUBSTRATE PEPTIDE
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX / CELL CYCLE REGULATORY PROTEIN KINASE / THR160-PHOSPHO-CYCLIN DEPENDENT PROTEIN KINASE 2 IN ASSOCIATION WITH CYCLIN A / TRANSFERASE- TRANSFERASE SUBSTRATE COMPLEX
Function / homology
Function and homology information


: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon ...: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / positive regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / 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 / Y chromosome / cyclin-dependent protein kinase activity / 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 / microtubule organizing center / regulation of DNA replication / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / Activation of the pre-replicative complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cajal body / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / 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 / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / cellular response to estradiol stimulus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / DNA Damage/Telomere Stress Induced Senescence / potassium ion transport / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / chromosome, telomeric region / DNA replication / protein phosphorylation / endosome / Ub-specific processing proteases / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA-templated transcription / centrosome / protein kinase binding
Similarity search - Function
Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / 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
ADENOSINE-5'-TRIPHOSPHATE / NITRATE ION / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N.
Citation
Journal: Biochemistry / Year: 2002
Title: Structural Studies on Phospho-Cdk2/Cyclin a Bound to Nitrate, a Transition State Analogue: Implications for the Protein Kinase Mechanism
Authors: Cook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N.
#1: Journal: Nat.Cell Biol. / Year: 1999
Title: The Structural Basis for Specificity of Substrate and Recruitment Peptides Fo Cyclin-Dependent Kinases
Authors: Brown, N.R. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N.
History
DepositionApr 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 2.0May 15, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Other
Category: atom_site / database_PDB_rev ...atom_site / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 23, 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: SUBSTRATE PEPTIDE
F: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,57914
Polymers129,2086
Non-polymers1,3718
Water2,918162
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2897
Polymers64,6043
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
F: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2897
Polymers64,6043
Non-polymers6864
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.710, 164.100, 72.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99995, 0.00733, -0.00605), (0.00735, -0.9996, 0.00411), (-0.00602, -0.00415, -0.99997)
Vector: -0.28117, 155.81946, 36.73965)

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein CELL DIVISION PROTEIN KINASE 2 / P33 PROTEIN KINASE


Mass: 34143.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human)
Description: CDK2 WAS CO-EXPRESSED WITH CAK1 - PRODUCE THR160-PHOSPHO-CDK2
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P24941
#2: Protein CYCLIN A2


Mass: 29624.297 Da / Num. of mol.: 2 / Fragment: RESIDUES 175-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P20248

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide SUBSTRATE PEPTIDE


Mass: 835.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE HHASPRK / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 170 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsVAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT VAL D 175, N- ...VAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT VAL D 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT MODRES: 1GY3 TPO A 160() THR160 HAS BEEN PHOSPHORYLATED BY COEXPRESSION WITH CAK1 MODRES: 1GY3 TPO C 160() THR160 HAS BEEN PHOSPHORYLATED BY COEXPRESSION WITH CAK1

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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: 3.3 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 4C FROM SOLUTIONS CONTAINING 10 MG/ML PCDK2/CYCLIN A, 100 MM HEPES PH7.0, 2 MM SUBSTRATE PEPTIDE, 1MM ADP, 1.0 M LI2SO4. CRYSTALS WERE TRANSFERRED ...Details: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 4C FROM SOLUTIONS CONTAINING 10 MG/ML PCDK2/CYCLIN A, 100 MM HEPES PH7.0, 2 MM SUBSTRATE PEPTIDE, 1MM ADP, 1.0 M LI2SO4. CRYSTALS WERE TRANSFERRED TO 20%PEG 8K, 100 MM HEPES PH 7.0, 10 MM SUBSSTRATE PEPTIDE, 5 MM MG(NO3)2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlpCDK2/cyclinA1drop
2100 mMHEPES1droppH7.0
32 mMpeptide1drop
41 mMADP1drop
51.05-1.15 M1dropLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 45572 / % possible obs: 84.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 4.2
Reflection shellResolution: 2.7→2.81 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.5 / % possible all: 40.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 319218
Reflection shell
*PLUS
% possible obs: 40.7 %

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Processing

Software
NameClassification
REFMACmodel building
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QMZ

1qmz


Resolution: 2.7→20 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / ESU R Free: 0.42
RfactorNum. reflection% reflectionSelection details
Rfree0.313 -5.1 %RANDOM
Rwork0.25 ---
obs-41578 84.4 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9048 0 76 162 9286
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2

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