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- PDB-2cci: Crystal structure of phospho-CDK2 Cyclin A in complex with a pept... -

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Basic information

Entry
Database: PDB / ID: 2cci
TitleCrystal structure of phospho-CDK2 Cyclin A in complex with a peptide containing both the substrate and recruitment sites of CDC6
Components
  • Cell division control protein 6 homolog
  • Cyclin-A2
  • Cyclin-dependent kinase 2
KeywordsCELL CYCLE / COMPLEX (TRANSFERASE-CELL DIVISION) / PROTEIN KINASES / RECRUITMENT / SUBSTRATE RECOGNITION / ATP-BINDING / CELL DIVISION / KINASE / MITOSIS / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SERINE/THREONINE- PROTEIN KINASE / TRANSFERASE / CYCLIN / DNA REPLICATION / NUCLEAR PROTEIN / COMPLEX
Function / homology
Function and homology information


positive regulation of chromosome segregation / cellular response to vasopressin / CDC6 association with the ORC:origin complex / : / cyclin A2-CDK1 complex / traversing start control point of mitotic cell cycle / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / DNA replication checkpoint signaling / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 ...positive regulation of chromosome segregation / cellular response to vasopressin / CDC6 association with the ORC:origin complex / : / cyclin A2-CDK1 complex / traversing start control point of mitotic cell cycle / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / DNA replication checkpoint signaling / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic DNA replication checkpoint signaling / male pronucleus / female pronucleus / Transcription of E2F targets under negative control by DREAM complex / cellular response to cocaine / response to glucagon / regulation of mitotic metaphase/anaphase transition / 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 / negative regulation of DNA replication / 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 cytokinesis / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / spindle midzone / X chromosome / G1/S-Specific Transcription / 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 / regulation of DNA replication / telomere maintenance in response to DNA damage / microtubule organizing center / centrosome duplication / cellular response to angiotensin / DNA replication origin binding / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / DNA replication initiation / 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 / intercellular bridge / 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 / protein serine/threonine kinase binding / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / Assembly of the pre-replicative complex / 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 / spindle pole / Cyclin D associated events in G1 / mitotic spindle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends
Similarity search - Function
Cell division protein Cdc6/18 / : / Cdc6/ORC-like, ATPase lid domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / Orc1-like, AAA ATPase domain / AAA ATPase domain / : / Cyclin-A, N-terminal APC/C binding region ...Cell division protein Cdc6/18 / : / Cdc6/ORC-like, ATPase lid domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / Orc1-like, AAA ATPase domain / AAA ATPase 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-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 / : / Winged helix DNA-binding domain 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 / Winged helix-like DNA-binding domain superfamily / Serine/Threonine protein kinases, catalytic domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cyclin-A2 / Cyclin-dependent kinase 2 / Cell division control protein 6 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCheng, K.Y. / Noble, M.E.M. / Skamnaki, V. / Brown, N.R. / Lowe, E.D. / Kontogiannis, L. / Shen, K. / Cole, P.A. / Siligardi, G. / Johnson, L.N.
CitationJournal: J. Biol. Chem. / Year: 2006
Title: The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition.
Authors: Cheng, K.Y. / Noble, M.E. / Skamnaki, V. / Brown, N.R. / Lowe, E.D. / Kontogiannis, L. / Shen, K. / Cole, P.A. / Siligardi, G. / Johnson, L.N.
History
DepositionJan 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 6, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_mod_residue.details
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 / pdbx_struct_conn_angle / 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 / _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
Revision 1.4Nov 13, 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: Cyclin-dependent kinase 2
B: Cyclin-A2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
F: Cell division control protein 6 homolog
I: Cell division control protein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,48010
Polymers134,4176
Non-polymers1,0634
Water2,000111
1
A: Cyclin-dependent kinase 2
B: Cyclin-A2
F: Cell division control protein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7405
Polymers67,2093
Non-polymers5312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
I: Cell division control protein 6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7405
Polymers67,2093
Non-polymers5312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.420, 114.389, 170.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Cyclin-dependent kinase 2 / 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 AT RESIDUE T160 / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A / Cyclin A


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) / Gene: CCNA2, CCN1, CCNA / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20248

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Protein/peptide , 1 types, 2 molecules FI

#3: Protein/peptide Cell division control protein 6 homolog / CDC6-related protein / Cdc18-related protein / HsCdc18 / p62(cdc6) / HsCDC6


Mass: 3440.896 Da / Num. of mol.: 2 / Fragment: RESIDUES 71-100 / Mutation: YES / Source method: obtained synthetically / Details: PEPTIDE MODIFIED TO GENERATE ACTIVE SITE SEQUENCE / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99741

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Non-polymers , 3 types, 115 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsINVOLVED IN THE CONTROL OF THE CELL CYCLE ENGINEERED RESIDUE IN CHAIN F, PRO 71 TO HIS ENGINEERED ...INVOLVED IN THE CONTROL OF THE CELL CYCLE ENGINEERED RESIDUE IN CHAIN F, PRO 71 TO HIS ENGINEERED RESIDUE IN CHAIN F, PRO 72 TO HIS ENGINEERED RESIDUE IN CHAIN F, CYS 73 TO ALA ENGINEERED RESIDUE IN CHAIN F, PRO 76 TO ARG ENGINEERED RESIDUE IN CHAIN I, PRO 71 TO HIS ENGINEERED RESIDUE IN CHAIN I, PRO 72 TO HIS ENGINEERED RESIDUE IN CHAIN I, CYS 73 TO ALA ENGINEERED RESIDUE IN CHAIN I, PRO 76 TO ARG
Has protein modificationY
Sequence detailsCHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING OF RESIDUES 175-432 THE PEPTIDE ...CHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING OF RESIDUES 175-432 THE PEPTIDE CONTAINS RESIDUES 71-100 OF CDC6 WITH THE FIRST SEVEN PEPTIDES MODIFIED TO GENERATE AN IDEAL SUBSTRATE

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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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.6
Details: 10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 39629 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMZ

1qmz


Resolution: 2.7→94.92 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.775 / SU B: 34.164 / SU ML: 0.347 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 12.217 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.321 1996 5 %RANDOM
Rwork0.261 ---
obs0.264 37597 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--0.5 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.7→94.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9216 0 64 111 9391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229509
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.98612917
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33751135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45723.735407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.831550
X-RAY DIFFRACTIONr_chiral_restr0.0770.21459
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.24507
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.26433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2337
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2851.55888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.50629300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.65734105
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1044.53617
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.432 154
Rwork0.356 2760
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)
11.50960.75490.2031.9782-0.15751.3512-0.08730.08570.2090.04090.03820.1389-0.2132-0.10910.0491-0.28530.032-0.021-0.1761-0.0102-0.182925.375540.83993.3747
21.6144-0.6575-0.52652.35640.32421.6912-0.0607-0.1652-0.04430.18250.0320.0236-0.02590.06180.0287-0.2469-0.0097-0.0175-0.1294-0.009-0.290641.146838.476932.4078
33.1107-0.702-1.26621.88220.2111.90670.05830.27980.2579-0.2011-0.10040.2718-0.4407-0.45930.04210.04350.1156-0.04220.071-0.0075-0.01528.737521.789654.1547
43.3876-0.2582-0.25032.37070.16641.5269-0.2111-0.1738-0.11590.45790.08350.42070.0126-0.31510.12760.11410.05510.1119-0.06720.014-0.050110.871610.644185.3526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 296
2X-RAY DIFFRACTION2B175 - 432
3X-RAY DIFFRACTION3C0 - 296
4X-RAY DIFFRACTION4D175 - 432

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