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- PDB-6q38: The Crystal structure of CK2a bound to P1-C4 -

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Basic information

Entry
Database: PDB / ID: 6q38
TitleThe Crystal structure of CK2a bound to P1-C4
Components
  • Casein kinase II subunit alpha
  • Stapled Peptide
KeywordsPEPTIDE BINDING PROTEIN / CK2alpha / CK2a / Stapled peptides / high concentration screening / selective ATP competitive inhibitors / surface entrophy reduction
Function / homology
Function and homology information


regulation of DNA binding / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of chromosome separation / protein kinase regulator activity / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL ...regulation of DNA binding / positive regulation of activin receptor signaling pathway / adiponectin-activated signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of chromosome separation / protein kinase regulator activity / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / negative regulation of blood vessel endothelial cell migration / negative regulation of apoptotic signaling pathway / positive regulation of SMAD protein signal transduction / peptidyl-threonine phosphorylation / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / fibrillar center / KEAP1-NFE2L2 pathway / positive regulation of protein catabolic process / rhythmic process / kinase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / protein-containing complex assembly / Regulation of TP53 Activity through Phosphorylation / secretory granule lumen / protein-macromolecule adaptor activity / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein domain specific binding / signaling receptor binding / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / Neutrophil degranulation / chromatin binding / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / Casein Kinase 2, subunit alpha / 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
Similarity search - Domain/homology
: / : / BENZOIC ACID / Casein kinase II subunit beta / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsBrear, P. / Iegre, J. / Baker, D. / Tan, Y. / Sore, H. / Donovan, D. / Spring, D. / Chandra, V. / Hyvonen, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust090340/Z/09/Z United Kingdom
Wellcome Trust107714/Z/15/Z United Kingdom
CitationJournal: Chem Sci / Year: 2019
Title: Efficient development of stable and highly functionalised peptides targeting the CK2 alpha /CK2 beta protein-protein interaction.
Authors: Iegre, J. / Brear, P. / Baker, D.J. / Tan, Y.S. / Atkinson, E.L. / Sore, H.F. / O' Donovan, D.H. / Verma, C.S. / Hyvonen, M. / Spring, D.R.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Mar 6, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_common_name / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_end / _struct_site_gen.label_asym_id
Revision 2.1Nov 13, 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: Casein kinase II subunit alpha
B: Stapled Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8714
Polymers40,4642
Non-polymers4062
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-5 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.887, 127.752, 54.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Casein kinase II subunit alpha / CK II alpha


Mass: 39118.617 Da / Num. of mol.: 1
Fragment: residues 2-329 and N-terminal extension GSMDIEFDDDADDDGSGSGSGSGS
Mutation: R21S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein/peptide Stapled Peptide


Type: Peptide-like / Class: Inhibitor / Mass: 1345.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: BIRD: PRD_002559, UniProt: P67870*PLUS
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-A1H27 / 3,5-bis(1-methyl-1,2,3-triazol-4-yl)benzoic acid


Type: Peptide-like / Class: Inhibitor / Mass: 284.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N6O2 / References: BIRD: PRD_002559
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.62 Å3/Da / Density % sol: 53.04 % / Mosaicity: 0.22 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M HEPES 7.5 pH, 10 %w/v PEG 8K, 8 %v/v Ethelyene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→63.88 Å / Num. obs: 44243 / % possible obs: 99.7 % / Redundancy: 18.8 % / Biso Wilson estimate: 30.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.041 / Rrim(I) all: 0.181 / Net I/σ(I): 11.1 / Num. measured all: 833029 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.74-1.8319.17.96512054163260.4191.8498.180.599.4
5.5-63.8815.90.0472446615410.9990.0120.04946.499.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.7.1data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OTZ

5otz


Resolution: 1.74→25.48 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2179 4.93 %RANDOM
Rwork0.204 ---
obs0.205 44161 99.4 %-
Displacement parametersBiso max: 158.32 Å2 / Biso mean: 56.92 Å2 / Biso min: 26.66 Å2
Baniso -1Baniso -2Baniso -3
1-7.5759 Å20 Å20 Å2
2---6.4957 Å20 Å2
3----1.0802 Å2
Refinement stepCycle: final / Resolution: 1.74→25.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 9 110 2997
Biso mean--49.45 47.41 -
Num. residues----336
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1067SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes463HARMONIC5
X-RAY DIFFRACTIONt_it2992HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion356SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3395SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2992HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4045HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion18.84
LS refinement shellResolution: 1.74→1.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2349 183 5.82 %
Rwork0.2144 2963 -
all0.2156 3146 -
obs--97.48 %
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)
12.3718-0.16610.03630.54730.23181.4154-0.06720.26670.1039-0.00840.0141-0.0816-0.00410.11450.0532-0.2806-0.0339-0.00080.3040.0372-0.3049.362432.849513.3899
21.86832.9104-0.33871.5581-1.52850.42230.0078-0.00930.02290.0078-0.0021-0.0485-0.06260.0031-0.0057-0.304-0.152-0.1520.08710.1520.30423.221462.44316.307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 329
2X-RAY DIFFRACTION2{ B|* }B1 - 15

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