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- PDB-2kji: A divergent ins protein in c. elegans structurally resemble insul... -

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Basic information

Entry
Database: PDB / ID: 2kji
TitleA divergent ins protein in c. elegans structurally resemble insulin and activates the human insulin receptor
ComponentsProbable insulin-like peptide beta-type 5
KeywordsHORMONE / INSULIN LIKE PEPTIDE / C. ELEGANS / FOLDING / ins-6 / Cleavage on pair of basic residues / Disulfide bond / Secreted
Function / homology
Function and homology information


cellular response to salt / negative regulation of dauer entry / dauer larval development / regulation of synaptic assembly at neuromuscular junction / chemosensory behavior / olfactory learning / insulin receptor binding / hormone activity / insulin receptor signaling pathway / extracellular space
Similarity search - Function
Nematode insulin-like peptide, beta type / : / Nematode insulin-related peptide beta type / Insulin-like, subunit E / Insulin-like / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable insulin-like peptide beta-type 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
Model detailsclosest to the average, model 1
AuthorsHua, Q.X. / Nakarawa, S.H. / Wilken, R. / Ramos, R.R. / Jia, W.H. / Bass, J. / Weiss, M.A.
CitationJournal: Genes Dev. / Year: 2003
Title: A divergent INS protein in Caenorhabditis elegans structurally resembles human insulin and activates the human insulin receptor.
Authors: Hua, Q.X. / Nakagawa, S.H. / Wilken, J. / Ramos, R.R. / Jia, W. / Bass, J. / Weiss, M.A.
History
DepositionMay 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable insulin-like peptide beta-type 5


Theoretical massNumber of molelcules
Total (without water)5,3041
Polymers5,3041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Probable insulin-like peptide beta-type 5


Mass: 5304.073 Da / Num. of mol.: 1 / Fragment: UNP residues 63-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ins-6, ZK84.6 / References: UniProt: P56174
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121NOESY
131COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES.

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Sample preparation

DetailsContents: 0.5 mM insulin-like peptide-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: insulin-like peptide-1
Sample conditionsIonic strength: 0.1 / pH: 7.4 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85BRUNGER, A.T. ET AL.refinement
VNMR_6.1B6.1BVarianstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: RMSD VALUES FOR ALL 20 STRUCTURES VERSUS GEOMETRIC AVERAGE: (BACKBONE, 5-23, 30-48) 0.41 ANGSTROM
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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