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- PDB-2n77: NMR solution structure of a complex of PEP-19 bound to the C-doma... -

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Basic information

Entry
Database: PDB / ID: 2n77
TitleNMR solution structure of a complex of PEP-19 bound to the C-domain of apo calmodulin
Components
  • Calmodulin
  • Purkinje cell protein 4
KeywordsSIGNALING PROTEIN / intrinsically disordered / structural transition
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 ...: / : / 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 / positive regulation of neuron differentiation / 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
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 regulator protein PCP4 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsWang, X. / Putkey, J.A.
CitationJournal: Nat Commun / Year: 2016
Title: PEP-19 modulates calcium binding to calmodulin by electrostatic steering.
Authors: Wang, X. / Putkey, J.A.
History
DepositionSep 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Aug 18, 2021Group: Data collection / Database references / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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
B: Purkinje cell protein 4


Theoretical massNumber of molelcules
Total (without water)15,2032
Polymers15,2032
Non-polymers00
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 / 300structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Calmodulin / CaM


Mass: 8416.203 Da / Num. of mol.: 1 / Fragment: EF-hand domains 3 and 4, residues 77-149
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) / Strain (production host): K12 / Variant (production host): BL21(DE3)pLysS / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein Purkinje cell protein 4 / Brain-specific antigen PCP-4 / Brain-specific polypeptide PEP-19


Mass: 6786.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCP4, PEP19 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21(DE3)pLysS / References: UniProt: P48539

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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 HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D C(CO)NH
1813D H(CCO)NH
1913D HBHA(CO)NH
11013D 1H-15N NOESY
11132D 1H-13C HSQC
11233D (H)CCH-TOCSY
11333D (H)CCH-COSY
11433D CCH-TOCSY
11533D 1H-13C NOESY aliphatic
11633D F1--filtered, F3-edited NOESY-HSQC
11722D 1H-15N HSQC
11823D HNCA
11923D HN(CO)CA
12023D CBCA(CO)NH
12123D HN(CA)CB
12223D HNCO
12323D 1H-15N NOESY
12423D C(CO)NH
12523D H(CCO)NH
12623D HBHA(CO)NH
12742D 1H-13C HSQC
12842D 1H-13C HSQC aromatic
12943D (H)CCH-TOCSY
13043D (H)CCH-COSY
13143D CCH-TOCSY
13243D 1H-13C NOESY aliphatic
1334D F1--filtered, F3-edited NOESY-HSQC
1345IPAP 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-100% 13C; U-100% 15N] C-CaM, 1.0 mM PEP_19, 100 mM potassium chloride, 5 mM [U-2H] EDTA, 10 uM [U-2H] DSS, 10 mM [U-2H] imidazole, 95% H2O/5% D2Osample_195% H2O/5% D2O
solution20.8 mM [U-100% 13C; U-100% 15N] PEP_19, 1.0 mM C-CaM, 100 mM potassium chloride, 5 mM [U-2H] EDTA, 10 uM [U-2H] DSS, 10 mM [U-2H] imidazole, 95% H2O/5% D2Osample_295% H2O/5% D2O
solution30.8 mM [U-100% 13C; U-100% 15N] C-CaM, 1.0 mM PEP_19, 100 mM potassium chloride, 5 mM [U-2H] EDTA, 10 uM [U-2H] DSS, 10 mM [U-2H] imidazole, 100% D2Osample_3100% D2O
solution40.8 mM [U-100% 13C; U-100% 15N] PEP, 1.0 mM C-CaM, 100 mM potassium chloride, 5 mM [U-2H] EDTA, 10 uM [U-2H] DSS, 10 mM [U-2H] imidazole, 100% D2Osample_4100% D2O
solution50.5 mM [U-99% 15N] C-CaM, 1.0 mM PEP_19, 5.0 mM [U-2H] EDTA, 5% C12E5 PEG, 100 mM potassium chloride, 10 mM [U-2H] imidazole, 95% H2O/5% D2Osample_595% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMC-CaM[U-100% 13C; U-100% 15N]1
1.0 mMPEP_19natural abundance1
100 mMpotassium chloridenatural abundance1
5 mMEDTA[U-2H]1
10 uMDSS[U-2H]1
10 mMimidazole[U-2H]1
0.8 mMPEP_19[U-100% 13C; U-100% 15N]2
1.0 mMC-CaMnatural abundance2
100 mMpotassium chloridenatural abundance2
5 mMEDTA[U-2H]2
10 uMDSS[U-2H]2
10 mMimidazole[U-2H]2
0.8 mMC-CaM[U-100% 13C; U-100% 15N]3
1.0 mMPEP_19natural abundance3
100 mMpotassium chloridenatural abundance3
5 mMEDTA[U-2H]3
10 uMDSS[U-2H]3
10 mMimidazole[U-2H]3
0.8 mMPEP-19[U-100% 13C; U-100% 15N]4
1.0 mMC-CaMnatural abundance4
100 mMpotassium chloridenatural abundance4
5 mMEDTA[U-2H]4
10 uMDSS[U-2H]4
10 mMimidazole[U-2H]4
0.5 mMC-CaM[U-99% 15N]5
1 mMPEP_19natural abundance5
5 mMEDTA[U-2H]5
5 %C12E5 PEGnatural abundance5
100 mMpotassium chloridenatural abundance5
10 mMimidazole[U-2H]5
Sample conditionsIonic strength: 0.1 / pH: 6.3 / Pressure: ambient / Temperature: 298 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
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
FelixAccelrys Software Inc.data analysis
FelixAccelrys Software Inc.processing
TopSpin2.1Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1917 / Hydrogen bond constraints total count: 98 / Protein other angle constraints total count: 0
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å

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