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- PDB-2n5r: NMR structure of cFLIP-derived calmodulin binding peptide -

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Basic information

Entry
Database: PDB / ID: 2n5r
TitleNMR structure of cFLIP-derived calmodulin binding peptide
ComponentsCASP8 and FADD-like apoptosis regulator
KeywordsAPOPTOSIS / calmodulin
Function / homology
Function and homology information


negative regulation of myoblast fusion / skeletal myofibril assembly / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 ...negative regulation of myoblast fusion / skeletal myofibril assembly / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of necroptotic process / positive regulation of extracellular matrix organization / skeletal muscle tissue regeneration / positive regulation of glomerular mesangial cell proliferation / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / negative regulation of hepatocyte apoptotic process / cysteine-type endopeptidase activity involved in execution phase of apoptosis / death receptor binding / positive regulation of hepatocyte proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / execution phase of apoptosis / RIPK1-mediated regulated necrosis / negative regulation of cardiac muscle cell apoptotic process / response to testosterone / cellular response to nitric oxide / negative regulation of reactive oxygen species biosynthetic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / skeletal muscle tissue development / keratinocyte differentiation / enzyme activator activity / cellular response to epidermal growth factor stimulus / cellular response to dexamethasone stimulus / erythrocyte differentiation / cellular response to estradiol stimulus / negative regulation of extrinsic apoptotic signaling pathway / Regulation of TNFR1 signaling / wound healing / neuron differentiation / positive regulation of neuron projection development / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / positive regulation of NF-kappaB transcription factor activity / cellular response to hypoxia / positive regulation of canonical NF-kappaB signal transduction / protease binding / positive regulation of ERK1 and ERK2 cascade / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / proteolysis / cytoplasm / cytosol
Similarity search - Function
Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain ...Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
CASP8 and FADD-like apoptosis regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailsclosest to the average, model7
AuthorsPanaitiu, A.E.
CitationJournal: Plos One / Year: 2015
Title: Identification and Characterization of the Interaction Site between cFLIPL and Calmodulin.
Authors: Gaidos, G. / Panaitiu, A.E. / Guo, B. / Pellegrini, M. / Mierke, D.F.
History
DepositionJul 24, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Revision 1.2May 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: CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)1,5621
Polymers1,5621
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)21 / 97structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide CASP8 and FADD-like apoptosis regulator / Caspase homolog / CASH / Caspase-eight-related protein / Casper / Caspase-like apoptosis regulatory ...Caspase homolog / CASH / Caspase-eight-related protein / Casper / Caspase-like apoptosis regulatory protein / CLARP / Cellular FLICE-like inhibitory protein / c-FLIP / FADD-like antiapoptotic molecule 1 / FLAME-1 / Inhibitor of FLICE / I-FLICE / MACH-related inducer of toxicity / MRIT / Usurpin / CASP8 and FADD-like apoptosis regulator subunit p43 / CASP8 and FADD-like apoptosis regulator subunit p12


Mass: 1561.980 Da / Num. of mol.: 1 / Fragment: DED 1 domain residues 62-73 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15519

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 20 mM potassium phosphate, 150 mM sodium chloride, 1 mM calcium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMpotassium phosphate-11
150 mMsodium chloride-21
1 mMcalcium chloride-31
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 288 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
NameDeveloperClassification
SparkyGoddardchemical shift assignment
in-house_softwareDale F. Mierkerefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 97 / Conformers submitted total number: 21

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