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- PDB-2n27: Competitive inhibition of TRPV1 calmodulin interaction by vanilloids -

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Basic information

Entry
Database: PDB / ID: 2n27
TitleCompetitive inhibition of TRPV1 calmodulin interaction by vanilloids
ComponentsCalmodulin
KeywordsMETAL BINDING PROTEIN / calmodulin / capsaicin
Function / homology
Function and homology information


: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / 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 / regulation of synaptic vesicle exocytosis / 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 / response to corticosterone / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / adenylate cyclase binding / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / eNOS activation / Protein methylation / voltage-gated potassium channel complex / activation of adenylate cyclase activity / enzyme regulator activity / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / nitric-oxide synthase regulator activity / substantia nigra development / adenylate cyclase activator activity / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of nitric-oxide synthase activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrial membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / synaptic vesicle membrane / response to calcium ion
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
Chem-4DY / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsHetenyi, A. / Nemeth, L. / Weber, E. / Szakonyi, G. / Winter, Z. / Josvay, K. / Bartus, E. / Olah, Z. / Martinek, T.A.
CitationJournal: Febs Lett. / Year: 2016
Title: Competitive inhibition of TRPV1-calmodulin interaction by vanilloids.
Authors: Hetenyi, A. / Nemeth, L. / Weber, E. / Szakonyi, G. / Winter, Z. / Josvay, K. / Bartus, E. / Olah, Z. / Martinek, T.A.
History
DepositionApr 29, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Structure summary
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1876
Polymers16,7211
Non-polymers4665
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 #1fewest violations

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1 / Fragment: UNP residues 2-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-4DY / (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide / Capsaicin / 8-Methyl-N-vanillyl-trans-6-nonenamide / NGX-4010


Mass: 305.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27NO3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
160 uM [U-98% 13C; U-98% 15N] Calmodulin, 90% H2O/10% D2O90% H2O/10% D2O
260 uM [U-98% 13C; U-98% 15N] Calmodulin, 300 uM capsaicin, 90% H2O/10% D2O90% H2O/10% D2O
360 uM [U-98% 13C; U-98% 15N] Calmodulin, 180 uM resiniferatoxin, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
60 uMCalmodulin-1[U-98% 13C; U-98% 15N]1
60 uMCalmodulin-2[U-98% 13C; U-98% 15N]2
300 uMcapsaicin-32
60 uMCalmodulin-4[U-98% 13C; U-98% 15N]3
180 uMresiniferatoxin-53
Sample conditionsIonic strength: 30 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TopSpin3.1Bruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 519 / NOE intraresidue total count: 82 / NOE long range total count: 50 / NOE medium range total count: 57 / NOE sequential total count: 90 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 103 / Protein psi angle constraints total count: 103
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 20

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