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- PDB-2n99: Solution structure of the SLURP-2, a secreted isoform of Lynx1 -

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Basic information

Entry
Database: PDB / ID: 2n99
TitleSolution structure of the SLURP-2, a secreted isoform of Lynx1
ComponentsLy-6/neurotoxin-like protein 1
KeywordsNEUROPEPTIDE / neuromodulator / cell proliferation / three-finger protein / nicotinic acetylcholine receptor / muscarinic acetylcholine receptor / epithelium / keratinocyte
Function / homology
Function and homology information


regulation of neurotransmitter receptor activity / acetylcholine receptor regulator activity / : / acetylcholine receptor inhibitor activity / acetylcholine receptor binding / acetylcholine receptor signaling pathway / dendrite / synapse / endoplasmic reticulum / extracellular space ...regulation of neurotransmitter receptor activity / acetylcholine receptor regulator activity / : / acetylcholine receptor inhibitor activity / acetylcholine receptor binding / acetylcholine receptor signaling pathway / dendrite / synapse / endoplasmic reticulum / extracellular space / membrane / plasma membrane
Similarity search - Function
Snake toxin/toxin-like / Ly-6 antigen / uPA receptor -like domain / Snake toxin and toxin-like protein / u-PAR/Ly-6 domain / Ly-6 antigen/uPA receptor-like / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Secreted Ly-6/uPAR domain-containing protein 2 / Ly-6/neurotoxin-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsParamonov, A.S. / Shenkarev, Z.O. / Lyukmanova, E.N. / Arseniev, A.S.
CitationJournal: Sci Rep / Year: 2016
Title: Secreted Isoform of Human Lynx1 (SLURP-2): Spatial Structure and Pharmacology of Interactions with Different Types of Acetylcholine Receptors.
Authors: Lyukmanova, E.N. / Shulepko, M.A. / Shenkarev, Z.O. / Bychkov, M.L. / Paramonov, A.S. / Chugunov, A.O. / Kulbatskii, D.S. / Arvaniti, M. / Dolejsi, E. / Schaer, T. / Arseniev, A.S. / ...Authors: Lyukmanova, E.N. / Shulepko, M.A. / Shenkarev, Z.O. / Bychkov, M.L. / Paramonov, A.S. / Chugunov, A.O. / Kulbatskii, D.S. / Arvaniti, M. / Dolejsi, E. / Schaer, T. / Arseniev, A.S. / Efremov, R.G. / Thomsen, M.S. / Dolezal, V. / Bertrand, D. / Dolgikh, D.A. / Kirpichnikov, M.P.
History
DepositionNov 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ly-6/neurotoxin-like protein 1


Theoretical massNumber of molelcules
Total (without water)8,1631
Polymers8,1631
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 / 500target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Ly-6/neurotoxin-like protein 1 / Secreted Ly-6/uPAR domain-containing protein 2 / Secreted Ly-6/uPAR-related protein 2 / SLURP-2


Mass: 8163.424 Da / Num. of mol.: 1 / Fragment: residues 57-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYNX1, SLURP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9BZG9, UniProt: P0DP57*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HN(CO)CA
1713D (H)CCH-TOCSY
1813D HNHA
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-15N TOCSY
11213D HNHB

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] SLURP, 95% H2O/5% D2O/5% dioxane-d6
Solvent system: 95% H2O/5% D2O/5% dioxane-d6
SampleConc.: 0.5 mM / Component: SLURP-2-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 10 / pH: 5.0 / Pressure: ambient / Temperature: 315 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
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20

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