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- PDB-2k0e: A Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Sign... -

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Basic information

Entry
Database: PDB / ID: 2k0e
TitleA Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Signal Transduction
ComponentsCalmodulin
KeywordsMETAL BINDING PROTEIN / EF HANDS / ENSEMBLE / HELIX BUNDLE / CALCIUM BINDING
Function / homology
Function and homology information


: / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of peptidyl-threonine phosphorylation / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...: / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of peptidyl-threonine phosphorylation / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / 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 / PKA activation / positive regulation of DNA binding / 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) / nitric-oxide synthase binding / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / 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 ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / positive regulation of protein autophosphorylation / Long-term potentiation / protein phosphatase activator activity / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / 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 / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / activation of adenylate cyclase activity / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / FCERI mediated Ca+2 mobilization / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of nitric-oxide synthase activity / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / mitochondrial membrane / cellular response to type II interferon
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-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / CHARMM
Model detailsSTRUCTURES DETERMINED WITH THE MUMO METHOD (MINIMALUNDER-RESTRAINING MINIMAL OVER-RESTRAINING
AuthorsGsponer, J. / Christodoulou, J. / Cavalli, A. / Bui, J.M. / Richter, B. / Dobson, C.M. / Vendruscolo, M.
CitationJournal: Structure / Year: 2008
Title: A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction
Authors: Gsponer, J. / Christodoulou, J. / Cavalli, A. / Bui, J.M. / Richter, B. / Dobson, C.M. / Vendruscolo, M.
History
DepositionFeb 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8825
Polymers16,7211
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)160 / 160all calculated structures submitted
RepresentativeModel #1

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Components

#1: Protein Calmodulin


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) / 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: STRUCTURES DETERMINED WITH THE MUMO METHOD (MINIMALUNDER-RESTRAINING MINIMAL OVER-RESTRAINING

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Sample preparation

DetailsContents: 0.5 mM Calmodulin
SampleConc.: 0.5 mM / Component: Calmodulin
Sample conditionsPressure units: atm / Temperature units: K

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NMR measurement

NMR spectrometerType: NULL NULL

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Processing

NMR softwareName: CHARMM / Version: C30
Developer: B.R.BROOKS, R.E.BRUCCOLERI, B.D.OLAFSON,D.J.STATES, S.SWAMINATHAN, M.KARLPLUS
Classification: refinement
RefinementMethod: CHARMM / Software ordinal: 1
Details: PROGRAM : CHARMM C30 AUTHORS : B.R.BROOKS, R.E.BRUCCOLERI, B.D.OLAFSON,D.J.STATES, S.SWAMINATHAN, M.KARLPLUS
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 160 / Conformers submitted total number: 160

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