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- PDB-2jzi: Structure of Calmodulin complexed with the Calmodulin Binding Dom... -

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Basic information

Entry
Database: PDB / ID: 2jzi
TitleStructure of Calmodulin complexed with the Calmodulin Binding Domain of Calcineurin
Components
  • Calmodulin
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsMETAL BINDING PROTEIN / Calcium binding protein / Acetylation / Methylation / Phosphoprotein / Ubl conjugation / Alternative splicing / Calmodulin-binding / Hydrolase / Iron / Metal-binding / Nucleus / Protein phosphatase / Zinc
Function / homology
Function and homology information


negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / positive regulation of saliva secretion / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane ...negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / positive regulation of saliva secretion / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane / slit diaphragm / positive regulation of cardiac muscle hypertrophy in response to stress / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / renal filtration / calcineurin-NFAT signaling cascade / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / skeletal muscle tissue regeneration / transition between fast and slow fiber / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / extrinsic component of plasma membrane / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / dendrite morphogenesis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / dephosphorylation / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / protein serine/threonine phosphatase activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / regulation of synaptic vesicle exocytosis / myosin phosphatase activity / protein-serine/threonine phosphatase / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of activated T cell proliferation / RHO GTPases activate PAKs / calcineurin-mediated signaling / positive regulation of endocytosis / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / epidermis development / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission
Similarity search - Function
PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / EF-hand / : ...PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsChyan, C. / Huang, J. / Irene, D. / Lin, T.
CitationJournal: To be Published
Title: Structure of Calmodulin complexed with the Calmodulin Binding Domain of Calcineurin
Authors: Chyan, C. / Huang, J. / Irene, D. / Lin, T.
History
DepositionJan 9, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7026
Polymers19,5422
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform / Calmodulin-dependent calcineurin A subunit alpha isoform / CAM-PRP catalytic subunit


Mass: 2820.496 Da / Num. of mol.: 1
Fragment: UNP residues 391-414, Calmodulin_binding_domain_of_Calcineurin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q08209, protein-serine/threonine phosphatase
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D CBCANH
1713D C(CO)NH
1813D HBHA(CO)NH
1913D HNCO
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11312D DQF-COSY
11412D 1H-1H TOCSY
11512D 1H-1H NOESY
11613D H(CCO)NH

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] Calmodulin, 1 mM [U-99% 13C; U-99% 15N] Calmodulin binding domain of Calcineurin, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCalmodulin[U-99% 13C; U-99% 15N]1
1 mMCalmodulin binding domain of Calcineurin[U-99% 13C; U-99% 15N]1
Sample conditionspH: 6.5 / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Herrmann, Guntert and Wuthrichautomated noes assignment
CNS1.2refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 284 / Protein phi angle constraints total count: 142 / Protein psi angle constraints total count: 142
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Representative conformer: 1 / Torsion angle constraint violation method: TALOS

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