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- PDB-2kdt: PC1/3 DCSG sorting domain structure in DPC -

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Basic information

Entry
Database: PDB / ID: 2kdt
TitlePC1/3 DCSG sorting domain structure in DPC
ComponentsNeuroendocrine convertase 1
KeywordsPROTEIN TRANSPORT / secretory granules / prohorme convertase / Calcium / Cleavage on pair of basic residues / Cytoplasmic vesicle / Glycoprotein / Hydrolase / Protease / Serine protease / Zymogen
Function / homology
Function and homology information


proprotein convertase 1 / Peptide hormone biosynthesis / Synthesis, secretion, and deacylation of Ghrelin / insulin processing / response to chlorate / peptide biosynthetic process / pituitary gland development / response to fatty acid / pancreas development / peptide hormone processing ...proprotein convertase 1 / Peptide hormone biosynthesis / Synthesis, secretion, and deacylation of Ghrelin / insulin processing / response to chlorate / peptide biosynthetic process / pituitary gland development / response to fatty acid / pancreas development / peptide hormone processing / protein autoprocessing / response to axon injury / response to glucose / axon terminus / response to glucocorticoid / transport vesicle / response to interleukin-1 / neurogenesis / response to nutrient levels / secretory granule / positive regulation of protein secretion / trans-Golgi network / protein processing / response to peptide hormone / response to calcium ion / perikaryon / secretory granule lumen / endopeptidase activity / response to lipopolysaccharide / neuron projection / response to xenobiotic stimulus / endoplasmic reticulum lumen / serine-type endopeptidase activity / neuronal cell body / dendrite / perinuclear region of cytoplasm / extracellular space / membrane / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3320 / Prohormone convertase enzyme / Prohormone convertase enzyme / Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3320 / Prohormone convertase enzyme / Prohormone convertase enzyme / Peptidase S8, pro-domain / Peptidase S8, pro-domain superfamily / Peptidase S8 pro-domain / Kexin/furin catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Helix non-globular / Galactose-binding-like domain superfamily / Special
Similarity search - Domain/homology
Neuroendocrine convertase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDikeakos, J.D. / Di Lello, P. / Lacombe, M.J. / Ghirlando, R. / Legault, P. / Reudelhuber, T.L. / Omichinski, J.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Functional and structural characterization of a dense core secretory granule sorting domain from the PC1/3 protease.
Authors: Dikeakos, J.D. / Di Lello, P. / Lacombe, M.J. / Ghirlando, R. / Legault, P. / Reudelhuber, T.L. / Omichinski, J.G.
History
DepositionJan 19, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 22, 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: Neuroendocrine convertase 1


Theoretical massNumber of molelcules
Total (without water)5,2761
Polymers5,2761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Neuroendocrine convertase 1 / NEC 1 / Prohormone convertase 1 / Proprotein convertase 1 / PC1 / PC3 / Furin homolog / Propeptide- ...NEC 1 / Prohormone convertase 1 / Proprotein convertase 1 / PC1 / PC3 / Furin homolog / Propeptide-processing protease


Mass: 5275.727 Da / Num. of mol.: 1 / Fragment: DCSG sorting domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species: musculus / Gene: Pcsk1, Att-1, Nec-1, Nec1 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: P63239, proprotein convertase 1

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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(CA)CB
1513D HBHA(CO)NH
1613D HN(CO)CA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 15N] PC1/3 DCSG-sorting domain, 1 mM [U-100% 13C; U-100% 15N] PC1/3 DCSG-sorting domain, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPC1/3 DCSG-sorting domain[U-100% 15N]1
1 mMPC1/3 DCSG-sorting domain[U-100% 13C; U-100% 15N]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Varian UnityVarianUNITY8002
Varian UnityVarianUNITY6003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRViewJohnson, One Moon Scientificchemical shift assignment
VNMRVariancollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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