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Yorodumi- PDB-6zss: NMR structure of water-soluble domain of human Lynx2 (Lypd1) protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zss | ||||||
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Title | NMR structure of water-soluble domain of human Lynx2 (Lypd1) protein | ||||||
Components | Ly6/PLAUR domain-containing protein 1 | ||||||
Keywords | NEUROPEPTIDE / 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 / acetylcholine receptor signaling pathway / negative regulation of protein localization to plasma membrane / synaptic transmission, cholinergic / behavioral fear response / response to nicotine / synapse ...: / Post-translational modification: synthesis of GPI-anchored proteins / acetylcholine receptor inhibitor activity / acetylcholine receptor binding / acetylcholine receptor signaling pathway / negative regulation of protein localization to plasma membrane / synaptic transmission, cholinergic / behavioral fear response / response to nicotine / synapse / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kocharovskaya, M.V. / Paramonov, A.S. / Lyukmanova, E.N. / Shenkarev, Z.O. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zss.cif.gz | 486.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zss.ent.gz | 408.9 KB | Display | PDB format |
PDBx/mmJSON format | 6zss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zss ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zss | HTTPS FTP |
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-Related structure data
Related structure data | 6ib6C 6zsoC 6zzeC 6zzfC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 |
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Sample | Conc.: 0.25 mM / Component: Lynx2 / Isotopic labeling: [U-98% 13C; U-98% 15N] |
Sample conditions | Ionic strength: 10 mM / Ionic strength err: 5 / Label: conditions1 / pH: 6.7 / Pressure: AMBIENT Pa / Temperature: 318 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz / Details: CryoProbe |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |