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- PDB-6zss: NMR structure of water-soluble domain of human Lynx2 (Lypd1) protein -

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Basic information

Entry
Database: PDB / ID: 6zss
TitleNMR structure of water-soluble domain of human Lynx2 (Lypd1) protein
ComponentsLy6/PLAUR domain-containing protein 1
KeywordsNEUROPEPTIDE / Ly-6 / Ly6/uPAR / three-finger protein / nicotinic acetylcholine receptor / Lynx / Lynx2 / Lypd1 / snake neurotoxin
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / acetylcholine receptor inhibitor activity / acetylcholine receptor binding / synaptic transmission, cholinergic / acetylcholine receptor signaling pathway / negative regulation of protein localization to plasma membrane / behavioral fear response / side of membrane / protein localization to plasma membrane / response to nicotine ...Post-translational modification: synthesis of GPI-anchored proteins / acetylcholine receptor inhibitor activity / acetylcholine receptor binding / synaptic transmission, cholinergic / acetylcholine receptor signaling pathway / negative regulation of protein localization to plasma membrane / behavioral fear response / side of membrane / protein localization to plasma membrane / response to nicotine / synapse / extracellular region / plasma membrane
Similarity search - Function
Snake toxin-like superfamily
Similarity search - Domain/homology
Ly6/PLAUR domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKocharovskaya, M.V. / Paramonov, A.S. / Lyukmanova, E.N. / Shenkarev, Z.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20176 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors.
Authors: Paramonov, A.S. / Kocharovskaya, M.V. / Tsarev, A.V. / Kulbatskii, D.S. / Loktyushov, E.V. / Shulepko, M.A. / Kirpichnikov, M.P. / Lyukmanova, E.N. / Shenkarev, Z.O.
History
DepositionJul 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: 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 1.2Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ly6/PLAUR domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)9,3911
Polymers9,3911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5740 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Ly6/PLAUR domain-containing protein 1 / Putative HeLa tumor suppressor / PHTS


Mass: 9390.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPD1, LYPDC1, PSEC0181, UNQ3079/PRO9917 / Plasmid: pET-22b(+) / Cell line (production host): SHuffle / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N2G4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HN(CA)CO
1101isotropic13D HNCA
1111isotropic13D HN(CO)CA
131isotropic13D HN(CA)CB
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC
171isotropic13D 1H-15N-NOESY-HSQC
161isotropic13D 1H-15N-TOCSY-HSQC
181isotropic13D 1H-13C-(H)CCH-TOCSY
191isotropic13D HNHA
1121isotropic13D HNHB
1131isotropic12D 1H-13C TROSY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O
Label: 13C_15N_sample1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.25 mM / Component: Lynx2 / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 10 mM / Ionic strength err: 5 / Label: conditions1 / pH: 6.7 / Pressure: AMBIENT Pa / Temperature: 318 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
TopSpinBruker Biospincollection
CARA1.8Keller and Wuthrichchemical shift assignment
MddNMRV. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, Swedish NMR Center, University of Gothenburgprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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