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- PDB-2kne: Calmodulin wraps around its binding domain in the plasma membrane... -

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Basic information

Entry
Database: PDB / ID: 2kne
TitleCalmodulin wraps around its binding domain in the plasma membrane CA2+ pump anchored by a novel 18-1 motif
Components
  • ATPase, Ca++ transporting, plasma membrane 4
  • Calmodulin
KeywordsMETAL TRANSPORT / protein/peptide / calcium pump / calmodulin / Acetylation / Calcium / Isopeptide bond / Methylation / Phosphoprotein / Polymorphism / Ubl conjugation / ATP-binding / Hydrolase / Membrane / Nucleotide-binding / Transmembrane
Function / homology
Function and homology information


negative regulation of the force of heart contraction / negative regulation of arginine catabolic process / negative regulation of cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / calcium ion transmembrane transporter activity / : / cellular response to acetylcholine / negative regulation of nitric oxide mediated signal transduction / nitric-oxide synthase inhibitor activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process ...negative regulation of the force of heart contraction / negative regulation of arginine catabolic process / negative regulation of cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / calcium ion transmembrane transporter activity / : / cellular response to acetylcholine / negative regulation of nitric oxide mediated signal transduction / nitric-oxide synthase inhibitor activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of peptidyl-cysteine S-nitrosylation / negative regulation of nitric-oxide synthase activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / sperm principal piece / calcium ion export / response to hydrostatic pressure / regulation of sodium ion transmembrane transport / flagellated sperm motility / P-type Ca2+ transporter / neural retina development / : / regulation of cell cycle G1/S phase transition / urinary bladder smooth muscle contraction / P-type calcium transporter activity / negative regulation of nitric oxide biosynthetic process / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / ATPase-coupled monoatomic cation transmembrane transporter activity / protein phosphatase 2B binding / positive regulation of cAMP-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / calcium ion transmembrane import into cytosol / regulation of synaptic vesicle endocytosis / negative regulation of cardiac muscle hypertrophy in response to stress / Calmodulin induced events / Reduction of cytosolic Ca++ levels / negative regulation of calcineurin-NFAT signaling cascade / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / plasma membrane => GO:0005886 / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / negative regulation of blood vessel endothelial cell migration / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / transport across blood-brain barrier / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / calcium ion import across plasma membrane / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac conduction / Smooth Muscle Contraction / sperm flagellum / sodium channel regulator activity / calcium channel inhibitor activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / presynaptic active zone membrane / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
Similarity search - Function
Plasma membrane calcium-transporting ATPase 4 / Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) ...Plasma membrane calcium-transporting ATPase 4 / Plasma membrane calcium transporting P-type ATPase, C-terminal / Plasma membrane calcium transporter ATPase C terminal / P-type ATPase, subfamily IIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / EF-hand / Recoverin; domain 1 / HAD superfamily / HAD-like superfamily / 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
Plasma membrane calcium-transporting ATPase 4 / Calmodulin-1 / Plasma membrane calcium-transporting ATPase 4 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsJuranic, N. / Atanasova, E. / Filoteo, A.G. / Macura, S. / Prendergast, F.G. / Penniston, J.T. / Strehler, E.E.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Calmodulin wraps around its binding domain in the plasma membrane Ca2+ pump anchored by a novel 18-1 motif.
Authors: Juranic, N. / Atanasova, E. / Filoteo, A.G. / Macura, S. / Prendergast, F.G. / Penniston, J.T. / Strehler, E.E.
History
DepositionAug 21, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _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
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin
B: ATPase, Ca++ transporting, plasma membrane 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2426
Polymers20,0812
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
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) / Strain: BL21(DE3)-pLysS
Gene: CALM, CALM1, CALM2, CALM3, CALML2, CAM, CAM1, CAM2, CAM3, CAMB, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide ATPase, Ca++ transporting, plasma membrane 4


Mass: 3359.993 Da / Num. of mol.: 1 / Fragment: UNP residues 1086-1113, C28
Source method: isolated from a genetically manipulated source
Details: calmodulin binding domain of PMCA C-tail / Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3) / Gene: ATP2B4, hCG_18445, RP11-397P13.1-001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: B1APW6, UniProt: P23634*PLUS
#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
Details: Structure of holo-calmodulin in complex with C28 peptide from C-tail calmodulin-binding-domain of plasma-membrane-calcium-pump
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1223D HNCO
1313D HN(CA)CB
1423D HN(CA)CB
1513D CBCA(CO)NH
1623D CBCA(CO)NH
1713D (H)CCH-TOCSY
1823D (H)CCH-TOCSY
1913D HBHA(CO)NH
11023D HBHA(CO)NH
11113D (H)CCH-COSY
11223D (H)CCH-COSY
11313D 1H-15N NOESY
11423D 1H-15N NOESY
11513D 1H-13C NOESY
11623D 1H-13C NOESY
21713D HNCO
21823D HNCO
11913D HNHA
12023D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-99% 13C; U-99% 15N] entity_1-1, 95% H2O/5% D2O95% H2O/5% D2O
21-2 mM [U-99% 13C; U-99% 15N] entity_1-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-99% 13C; U-99% 15N]1-21
mMentity_1-2[U-99% 13C; U-99% 15N]1-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 7.5 ambient atm298 K
20.1 7.5 ambient atm298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
FelixFelix NMR 2007Accelrys Software Inc.processing
FelixFelix NMR 2007Accelrys Software Inc.peak picking
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thogeometry optimization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorefinement
PREDITORBerjanskii MV, Neal S, Wishart DSdata analysis
PREDITORBerjanskii MV, Neal S, Wishart DStorsion angles prediction
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT ALSO USES THE PROTEIN (CALMODULIN) & PEPTIDE (C28) RESIDUAL DIPOLAR COUPLINGS (BACKBONE NH, NCO and COCA) MEASURED IN A PHAGE-FILAMENTS ORIENTED MEDIA.
NMR constraintsNOE constraints total: 2446 / NOE intraresidue total count: 1113 / NOE long range total count: 315 / NOE medium range total count: 355 / NOE sequential total count: 664 / Protein other angle constraints total count: 136 / Protein phi angle constraints total count: 154 / Protein psi angle constraints total count: 150
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: -0.7 Å / Maximum torsion angle constraint violation: 10 ° / Maximum upper distance constraint violation: 0.6 Å / Torsion angle constraint violation method: XPLOR-NIH
NMR ensemble rmsDistance rms dev: 0.055 Å / Distance rms dev error: 0.005 Å

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