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- PDB-7d13: NERP-2 in a HFIP solution -

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Basic information

Entry
Database: PDB / ID: 7d13
TitleNERP-2 in a HFIP solution
ComponentsNeurosecretory protein VGF
KeywordsNEUROPEPTIDE / VGF / Energy homeostasis
Function / homology
Function and homology information


carbohydrate homeostasis / synaptic signaling via neuropeptide / sexual reproduction / neuropeptide hormone activity / NGF-stimulated transcription / insulin secretion / regulation of neuronal synaptic plasticity / response to dietary excess / ovarian follicle development / response to cAMP ...carbohydrate homeostasis / synaptic signaling via neuropeptide / sexual reproduction / neuropeptide hormone activity / NGF-stimulated transcription / insulin secretion / regulation of neuronal synaptic plasticity / response to dietary excess / ovarian follicle development / response to cAMP / transport vesicle / response to cold / generation of precursor metabolites and energy / Post-translational protein phosphorylation / growth factor activity / response to insulin / regulation of synaptic plasticity / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose homeostasis / cytoplasmic vesicle / defense response to bacterium / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / Golgi apparatus / extracellular space
Similarity search - Function
Neurosecretory protein VGF
Similarity search - Domain/homology
Neurosecretory protein VGF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPark, O. / Cheong, C. / Jeon, Y.
Funding support1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)
CitationJournal: Peptide Science / Year: 2020
Title: Structure of neuroendocrine regulatory peptide-2 in membrane-mimicking environments.
Authors: Park, O. / Bang, J. / Ryu, K. / Hwang, E. / Hong, K. / Byun, Y. / Cheong, C. / Jeon, Y.
History
DepositionSep 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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: Neurosecretory protein VGF


Theoretical massNumber of molelcules
Total (without water)4,1741
Polymers4,1741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Neurosecretory protein VGF


Mass: 4173.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VGF / Production host: Escherichia coli (E. coli) / References: UniProt: O15240

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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
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D 1H-15N TOCSY
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM [U-13C; U-15N] NERP-2, 90% H2O/10% D2O
Details: 40% HFIP was added to provide a membrane-mimicking environment
Label: 15N,13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: NERP-2 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 25 mM sodium phosphate mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20
NMR ensemble rmsAtom type: all backbone atoms / Distance rms dev: 1.67 Å / Distance rms dev error: 0.48 Å

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