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- PDB-6ib6: Solution structure of the water-soluble LU-domain of human Lypd6 ... -

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Basic information

Entry
Database: PDB / ID: 6ib6
TitleSolution structure of the water-soluble LU-domain of human Lypd6 protein
ComponentsLy6/PLAUR domain-containing protein 6
KeywordsNEUROPEPTIDE / Lypd6 / Ly6/uPAR / nicotinic acetylcholine receptor / three-finger proteins / SIGNALING PROTEIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / side of membrane / positive regulation of canonical Wnt signaling pathway / perikaryon / membrane raft / synapse / dendrite / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Ly6/PLAUR domain-containing protein 6-like / Ly6/PLAUR domain-containing protein 6, Lypd6 / Snake toxin-like superfamily
Similarity search - Domain/homology
Ly6/PLAUR domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTsarev, A.V. / Kulbatskii, D.S. / Paramonov, A.S. / Lyukmanova, E.N. / Shenkarev, Z.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research15-04-99517 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
DepositionNov 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 23, 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: Ly6/PLAUR domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)10,9411
Polymers10,9411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Ly6/PLAUR domain-containing protein 6


Mass: 10941.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal Met was added due to recombinant production
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPD6, UNQ3023/PRO9821 / Organ: Ubiquitous. Highly expressed in brain and heart / Plasmid: pET22b(+)/lypd6
Details (production host): Lypd6 coding sequence cloned into pET22b(+) between NdeI and HindIII sites
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86Y78
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
112isotropic23D 1H-15N NOESY
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic23D CBCA(CO)NH
151isotropic22D 1H-15N HSQC
161isotropic22D 1H-13C HSQC aliphatic
171isotropic23D HNCO
181isotropic23D (H)CCH-TOCSY
192isotropic22D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2OCN95% H2O/5% D2O
solution20.1 mM [U-99% 15N] Lypd6sh, 95% H2O/5% D2O15N95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMLypd6sh[U-99% 13C; U-99% 15N]1
0.1 mMLypd6sh[U-99% 15N]2
Sample conditionsIonic strength: 20 mM / Ionic strength err: 5 / Label: cond_1 / pH: 7 / PH err: 0.1 / Pressure: AMBIENT Pa / Temperature: 303 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001with CryoProbe
Bruker AVANCE IIIBrukerAVANCE III6002with CryoProbe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3.97Bruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
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: 500 / Conformers submitted total number: 20

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