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BMRB: 34532

6ZSS

NMR structure of water-soluble domain of human Lynx2 (Lypd1) protein

Authors

Kocharovskaya, M.V., Paramonov, A.S., Lyukmanova, E.N., Shenkarev, Z.O.

Assembly

Ly6/PLAUR domain-containing protein 1

Entity

1. Ly6/PLAUR domain-containing protein 1 (polymer, Thiol state: all disulfide bound), 86 monomers, 9386.719 Da Detail

MIQCYQCEEF QLNNDCSSPE FIVNCTVNVQ DMCQKEVMEQ SAGIMYRKSC ASSAACLIAS AGYQSFCSPG KLNSVCISCC NTPLCN

Formula weight

9386.719 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS33:SG
2	disulfide	sing	1:CYS7:SG	1:CYS16:SG
3	disulfide	sing	1:CYS25:SG	1:CYS50:SG
4	disulfide	sing	1:CYS56:SG	1:CYS79:SG
5	disulfide	sing	1:CYS67:SG	1:CYS76:SG
6	disulfide	sing	1:CYS80:SG	1:CYS85:SG

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 86.2 %, Completeness (bb): 90.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.2 % (815 of 946)	85.5 % (419 of 490)	86.3 % (309 of 358)	88.8 % (87 of 98)
Backbone	90.0 % (459 of 510)	88.4 % (152 of 172)	90.6 % (231 of 255)	91.6 % (76 of 83)
Sidechain	83.4 % (433 of 519)	84.0 % (267 of 318)	83.3 % (155 of 186)	73.3 % (11 of 15)
Aromatic	46.3 % (25 of 54)	59.3 % (16 of 27)	33.3 % (9 of 27)
Methyl	98.6 % (71 of 72)	97.2 % (35 of 36)	100.0 % (36 of 36)

1. entity 1

MIQCYQCEEF QLNNDCSSPE FIVNCTVNVQ DMCQKEVMEQ SAGIMYRKSC ASSAACLIAS AGYQSFCSPG KLNSVCISCC NTPLCN

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

Protein Blocks Logo

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

Release date

2020-08-12

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 1, : 1 : 6 : 5 entities Detail

Interaction partners 1. Ly6/PLAUR domain-containing protein 1, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 13 experiments Detail

1 3D HNCO

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

2 3D HNCACO

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

3 3D HNCACB

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

4 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

5 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

6 3D 1H-15N-TOCSY-HSQC

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

7 3D 1H-15N-NOESY-HSQC

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

8 3D 1H-13C-HCCH-TOCSY

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

9 3D HNHA

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

10 3D HNCA

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

11 3D HN(CO)CA

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

12 3D HNHB

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

13 2D 1H-13C TROSY aromatic

Instrument

Bruker AVANCE III - 800 MHz CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.7, Details 0.25 mM [U-98% 13C; U-98% 15N] Lynx2, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lynx2	[U-98% 13C; U-98% 15N]		0.25 (±0.03) mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34532_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:4:CYS:SG	1:33:CYS:SG	oxidized, CA 49.521, CB 39.89 ppm	oxidized, CA 49.854, CB 35.762 ppm	n/a
1:7:CYS:SG	1:16:CYS:SG	oxidized, CA 53.834, CB 42.819 ppm	oxidized, CA 53.254, CB 39.425 ppm	n/a
1:25:CYS:SG	1:50:CYS:SG	oxidized, CA 51.007, CB 34.008 ppm	oxidized, CA 55.746, CB 42.306 ppm	n/a
1:56:CYS:SG	1:79:CYS:SG	oxidized, CA 58.871, CB 39.893 ppm	oxidized, CA 51.448, CB 43.808 ppm	n/a
1:67:CYS:SG	1:76:CYS:SG	oxidized, CA 53.061, CB 35.397 ppm	oxidized, CA 52.154, CB 45.325 ppm	n/a
1:80:CYS:SG	1:85:CYS:SG	oxidized, CA 52.333, CB 43.552 ppm	oxidized, CA 53.791, CB 43.145 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34532_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	911		96.5 (chain: 1, length: 86)
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: 86, Sequence coverage: 96.5%
- Total number of assignments
  - ¹H chemical shifts: 512
  - ¹³C chemical shifts: 313
  - ¹⁵N chemical shifts: 86
- 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 Ly-6, Ly6/uPAR, Lynx, Lynx2, Lypd1, NEUROPEPTIDE, nicotinic acetylcholine receptor, snake neurotoxin, three-finger protein