BMRBj - BMREntryMaster

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BMRB: 34333

6IB6

Solution structure of the water-soluble LU-domain of human Lypd6 protein

Authors

Tsarev, A.V., Kulbatskii, D.S., Paramonov, A.S., Lyukmanova, E.N., Shenkarev, Z.O.

Assembly

Ly6/PLAUR domain-containing protein 6

Entity

1. Ly6/PLAUR domain-containing protein 6 (polymer), 96 monomers, 10928.22 Da Detail

MFKCFTCEKA ADNYECNRWA PDIYCPRETR YCYTQHTMEV TGNSISVTKR CVPLEECLST GCRDSEHEGH KVCTSCCEGN ICNLPLPRNE TDATFA

Formula weight

10928.22 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

LACS Plot; CA

Referencing offset: 2.6 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.6 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.65 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6IB6, Strand ID: A Detail

Release date

2018-12-09

Citation

Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors
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.
Int. J. Mol. Sci. (2020), 21, 7280-7280, PubMed 33019770 , DOI 10.3390/ijms21197280 , Abstract

Related entities 1. Ly6/PLAUR domain-containing protein 6, : 1 : 3 : 30 entities Detail

Interaction partners 1. Ly6/PLAUR domain-containing protein 6, : 4 interactors Detail

More details for 4 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	Lypd6sh	[U-99% 15N]		0.1 mM

2 3D HNCA

Instrument

Bruker AvanceIII - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lypd6sh	[U-99% 13C; U-99% 15N]		0.1 mM

3 3D HNCACB

Instrument

Bruker AvanceIII - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lypd6sh	[U-99% 13C; U-99% 15N]		0.1 mM

4 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lypd6sh	[U-99% 13C; U-99% 15N]		0.1 mM

5 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lypd6sh	[U-99% 13C; U-99% 15N]		0.1 mM

6 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lypd6sh	[U-99% 13C; U-99% 15N]		0.1 mM

7 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lypd6sh	[U-99% 13C; U-99% 15N]		0.1 mM

8 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 13C; U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lypd6sh	[U-99% 13C; U-99% 15N]		0.1 mM

9 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 7.0 (±0.1), Details 0.1 mM [U-99% 15N] Lypd6sh, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	Lypd6sh	[U-99% 15N]		0.1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34333_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34333_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1054		100.0 (chain: 1, length: 96)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 96, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 603
  - ¹³C chemical shifts: 354
  - ¹⁵N chemical shifts: 97
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords Ly6/uPAR, Lypd6, NEUROPEPTIDE, SIGNALING PROTEIN, nicotinic acetylcholine receptor, three-finger proteins