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- PDB-6p6c: CS-Rosetta Model of PEA-15 Death Effector Domain in the Complex w... -

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Basic information

Entry
Database: PDB / ID: 6p6c
TitleCS-Rosetta Model of PEA-15 Death Effector Domain in the Complex with ERK2
ComponentsAstrocytic phosphoprotein PEA-15
KeywordsAPOPTOSIS / protein-protein interaction / MAP kinase
Function / homology
Function and homology information


positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / RAF-independent MAPK1/3 activation / negative regulation of D-glucose import / microtubule associated complex / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / MAPK cascade / RAF/MAP kinase cascade / intracellular membrane-bounded organelle / apoptotic process / nucleoplasm / cytosol
Similarity search - Function
Astrocytic phosphoprotein PEA-15, death effector domain / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Astrocytic phosphoprotein PEA-15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWei, Y. / Crespo Flores, S. / Cabezas, A. / Hassan, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R21DA046223 United States
CitationJournal: Int J Mol Sci / Year: 2019
Title: PEA-15 C-Terminal Tail Allosterically Modulates Death-Effector Domain Conformation and Facilitates Protein-Protein Interactions.
Authors: Crespo-Flores, S.L. / Cabezas, A. / Hassan, S. / Wei, Y.
History
DepositionJun 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Astrocytic phosphoprotein PEA-15


Theoretical massNumber of molelcules
Total (without water)15,0611
Polymers15,0611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5430 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Astrocytic phosphoprotein PEA-15 / 15 kDa phosphoprotein enriched in astrocytes / Phosphoprotein enriched in diabetes / PED


Mass: 15061.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEA15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15121

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB

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Sample preparation

DetailsType: solution
Contents: 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM DTT, 50 uM sodium azide, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.1 mMDTTnatural abundance1
50 uMsodium azidenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10

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