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- PDB-6zso: Solution structure of the water-soluble LU-domain of human Lypd6b... -

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Basic information

Entry
Database: PDB / ID: 6zso
TitleSolution structure of the water-soluble LU-domain of human Lypd6b protein
ComponentsLy6/PLAUR domain-containing protein 6B
KeywordsNEUROPEPTIDE / Lypd6b / Ly6/uPAR / nicotinic acetylcholine receptor modulator / three-finger proteins
Function / homologyLy6/PLAUR domain-containing protein 6-like / Ly6/PLAUR domain-containing protein 6, Lypd6 / acetylcholine receptor regulator activity / Post-translational modification: synthesis of GPI-anchored proteins / Snake toxin-like superfamily / side of membrane / extracellular region / plasma membrane / Ly6/PLAUR domain-containing protein 6B
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTsarev, A.V. / Kulbatskii, D.S. / Paramonov, A.S. / Lyukmanova, E.N. / Shenkarev, Z.O.
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 1.1Nov 6, 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 6B


Theoretical massNumber of molelcules
Total (without water)11,0121
Polymers11,0121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7410 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1target function

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Components

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


Mass: 11012.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPD6B / Plasmid: pET22b(+)
Details (production host): coding sequence cloned into pET22b(+) between NdeI and HindIII sites
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NI32
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 1H-15N NOESY
121isotropic13D HNCO
131isotropic13D HN(CA)CB
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D HNHA
171isotropic23D HNHB
181isotropic13D (H)CCH-TOCSY
191isotropic12D 1H-13C HSQC aliphatic
1101isotropic12D 1H-15N HSQC
1111isotropic12d 1h-13C TROSY aromatic
1121isotropic13D CBCA(CO)NH

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Sample preparation

DetailsType: solution / Contents: 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O / Label: lypd6bCN / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.2 mM / Component: lypd6 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 10 mM / Ionic strength err: 5 / Label: sol1 / pH: 5.5 / PH err: 0.05 / 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
TopSpin3Bruker Biospincollection
MddNMRV. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, Swedish NMR Center, University of Gothenburgprocessing
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20

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