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- PDB-1ckk: CALMODULIN/RAT CA2+/CALMODULIN DEPENDENT PROTEIN KINASE FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1ckk
TitleCALMODULIN/RAT CA2+/CALMODULIN DEPENDENT PROTEIN KINASE FRAGMENT
Components
  • Calcium/calmodulin-dependent protein kinase kinase 1
  • Calmodulin-1
KeywordsCALMODULIN-PEPTIDE COMPLEX / COMPLEX (CALMODULIN-PEPTIDE) / CALMODULIN / CAMKK
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of RAC1 downstream of NMDARs / protein serine/threonine kinase activity => GO:0004674 / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / activation of protein kinase activity / positive regulation of protein kinase activity / calmodulin binding / intracellular signal transduction ...CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of RAC1 downstream of NMDARs / protein serine/threonine kinase activity => GO:0004674 / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / activation of protein kinase activity / positive regulation of protein kinase activity / calmodulin binding / intracellular signal transduction / signaling receptor binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / nucleoplasm / ATP binding / cytoplasm
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site ...EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calcium/calmodulin-dependent protein kinase kinase 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsOsawa, M. / Tokumitsu, H. / Swindells, M.B. / Kurihara, H. / Orita, M. / Shibanuma, T. / Furuya, T. / Ikura, M.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase.
Authors: Osawa, M. / Tokumitsu, H. / Swindells, M.B. / Kurihara, H. / Orita, M. / Shibanuma, T. / Furuya, T. / Ikura, M.
History
DepositionNov 20, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _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_seq_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-1
B: Calcium/calmodulin-dependent protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9056
Polymers19,7452
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100LOWEST ENERGY
Representative

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Components

#1: Protein Calmodulin-1 /


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: calm1 / Plasmid: PAS / Gene (production host): XENOPUS LAEVIS / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP33
#2: Protein/peptide Calcium/calmodulin-dependent protein kinase kinase 1 / CaMKK 1 / CaM-kinase IV kinase / Calcium/calmodulin-dependent protein kinase kinase alpha / CaMKK alpha


Mass: 3023.702 Da / Num. of mol.: 1 / Fragment: CALMODULIN BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: 26-RESIDUE SYNTHETIC PEPTIDE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Camkk1
References: UniProt: P97756, Ca2+/calmodulin-dependent protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsIonic strength: 100mM KCL, 10mM CACL2 / pH: 6.7 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8.5.1BRUNGERrefinement
X-PLOR3.8.5.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 30

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