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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 cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / negative regulation of arginine catabolic process / calcium ion transmembrane transporter activity / cellular response to acetylcholine / nitric-oxide synthase inhibitor activity / sperm principal piece / response to hydrostatic pressure / calcium ion export ...negative regulation of the force of heart contraction / negative regulation of cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / negative regulation of arginine catabolic process / calcium ion transmembrane transporter activity / cellular response to acetylcholine / nitric-oxide synthase inhibitor activity / sperm principal piece / response to hydrostatic pressure / calcium ion export / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / : / : / : / : / regulation of cell cycle G1/S phase transition / P-type Ca2+ transporter / : / positive regulation of protein autophosphorylation / P-type calcium transporter activity / neural retina development / regulation of sodium ion transmembrane transport / negative regulation of nitric oxide biosynthetic process / negative regulation of peptidyl-threonine phosphorylation / urinary bladder smooth muscle contraction / flagellated sperm motility / protein phosphatase 2B binding / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / negative regulation of calcineurin-NFAT signaling cascade / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of cardiac muscle hypertrophy in response to stress / response to corticosterone / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / calcium ion transmembrane import into cytosol / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcium ion import across plasma membrane / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / negative regulation of blood vessel endothelial cell migration / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / sodium channel regulator activity / Smooth Muscle Contraction / regulation of cardiac conduction / detection of calcium ion / catalytic complex / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / regulation of cytosolic calcium ion concentration / sperm flagellum / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / transport across blood-brain barrier / cellular response to interferon-beta / Protein methylation / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / nitric oxide-cGMP-mediated signaling / Activation of AMPK downstream of NMDARs / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
Similarity search - Function
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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain ...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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / 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)
10.17.5ambient atm298 K
20.17.5ambient 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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