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- PDB-2lqp: NMR solution structure of the Ca2+-Calmodulin C-terminal domain i... -

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Basic information

Entry
Database: PDB / ID: 2lqp
TitleNMR solution structure of the Ca2+-Calmodulin C-terminal domain in a complex with a peptide (NSCaTE) from the L-type Voltage-Gated Calcium Channel alpha1C subunit
ComponentsCalmodulin
KeywordsMETAL BINDING PROTEIN / NSCaTE
Function / homology
Function and homology information


: / : / : / : / : / : / positive regulation of protein autophosphorylation / transporter inhibitor activity / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding ...: / : / : / : / : / : / positive regulation of protein autophosphorylation / transporter inhibitor activity / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / positive regulation of peptidyl-threonine phosphorylation / positive regulation of DNA binding / positive regulation of protein serine/threonine kinase activity / response to corticosterone / CASP4 inflammasome assembly / negative regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of high voltage-gated calcium channel activity / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / nitric-oxide synthase binding / calcineurin-mediated signaling / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / protein phosphatase activator activity / regulation of calcium-mediated signaling / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / presynaptic cytosol / activation of adenylate cyclase activity / calcium channel inhibitor activity / positive regulation of nitric-oxide synthase activity / catalytic complex / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of heart rate / response to amphetamine / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / titin binding / calcium channel complex / voltage-gated potassium channel complex / substantia nigra development / protein serine/threonine kinase activator activity / sperm midpiece / calyx of Held / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / sarcomere / G2/M transition of mitotic cell cycle / myelin sheath / long-term synaptic potentiation / Enterobacterial factors antagonize host defense / response to calcium ion / disordered domain specific binding / mitochondrial membrane / calcium-dependent protein binding / synaptic vesicle membrane / growth cone / spindle pole / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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
Similarity search - Domain/homology
Calmodulin-2 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsLiu, Z. / Vogel, H.J.
CitationJournal: Front Mol Neurosci / Year: 2012
Title: Structural basis for the regulation of L-type voltage-gated calcium channels: interactions between the N-terminal cytoplasmic domain and Ca(2+)-calmodulin.
Authors: Liu, Z. / Vogel, H.J.
History
DepositionMar 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2363
Polymers8,1561
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / CaM


Mass: 8155.828 Da / Num. of mol.: 1 / Fragment: EF-hands 3 and 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP24*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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 aromatic
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY aliphatic
11013D 1H-15N NOESY
11113D HCACO
11212D 1H-15N HSQC
11313D HBHA(CO)NH

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Sample preparation

DetailsContents: 20 mM TRIS, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 20 mM / Component: TRIS-1
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
TALOSCornilescu, Delaglio and Baxchemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
XwinNMRBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 19

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