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BMRB: 34531

6ZSO

Solution structure of the water-soluble LU-domain of human Lypd6b protein

Authors

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

Assembly

Ly6/PLAUR domain-containing protein 6B

Entity

1. Ly6/PLAUR domain-containing protein 6B (polymer, Thiol state: all disulfide bound), 96 monomers, 10995.15 Da Detail

MFKCFTCENA GDNYNCNRWA EDKWCPQNTQ YCLTVHHFTS HGRSTSITKK CASRSECHFV GCHHSRDSEH TECRSCCEGM ICNVELPTNH TNAVFA

Formula weight

10995.15 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS32:SG
2	disulfide	sing	1:CYS7:SG	1:CYS16:SG
3	disulfide	sing	1:CYS25:SG	1:CYS51:SG
4	disulfide	sing	1:CYS57:SG	1:CYS76:SG
5	disulfide	sing	1:CYS62:SG	1:CYS73:SG
6	disulfide	sing	1:CYS77:SG	1:CYS82:SG

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 94.3 %, Completeness (bb): 96.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.3 % (1012 of 1073)	96.6 % (532 of 551)	90.8 % (373 of 411)	96.4 % (107 of 111)
Backbone	96.5 % (552 of 572)	97.4 % (189 of 194)	96.1 % (273 of 284)	95.7 % (90 of 94)
Sidechain	92.9 % (551 of 593)	96.1 % (343 of 357)	87.2 % (191 of 219)	100.0 % (17 of 17)
Aromatic	68.9 % (84 of 122)	80.3 % (49 of 61)	55.9 % (33 of 59)	100.0 % (2 of 2)
Methyl	100.0 % (60 of 60)	100.0 % (30 of 30)	100.0 % (30 of 30)

1. entity 1

MFKCFTCENA GDNYNCNRWA EDKWCPQNTQ YCLTVHHFTS HGRSTSITKK CASRSECHFV GCHHSRDSEH TECRSCCEGM ICNVELPTNH TNAVFA

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6ZSO, 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 6B, : 1 : 2 : 16 entities Detail

Experiments performed 12 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

2 3D HNCO

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

3 3D HNCACB

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

4 3D HNCA

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

5 3D HN(CO)CA

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

6 3D HNHA

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

7 3D HNHB

Instrument

Bruker AVANCE III - 600 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

8 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

10 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

11 2d 1h-13C TROSY aromatic

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

12 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 800 MHz with CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 5.5 (±0.05), Details 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	lypd6	[U-13C; U-15N]		0.2 (±0.02) mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34531_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	1:32:CYS:SG	oxidized, CA 50.219, CB 38.959 ppm	oxidized, CA 50.426, CB 35.571 ppm	n/a
1:7:CYS:SG	1:16:CYS:SG	oxidized, CA 53.076, CB 45.972 ppm	oxidized, CA 56.906, CB 41.017 ppm	n/a
1:25:CYS:SG	1:51:CYS:SG	oxidized, CA 49.51, CB 33.177 ppm	oxidized, CA 55.138, CB 39.842 ppm	n/a
1:57:CYS:SG	1:76:CYS:SG	oxidized, CA 52.851, CB 38.658 ppm	oxidized, CA 52.427, CB 46.621 ppm	n/a
1:62:CYS:SG	1:73:CYS:SG	oxidized, CA 52.871, CB 44.994 ppm	oxidized, CA 52.478, CB 44.695 ppm	n/a
1:77:CYS:SG	1:82:CYS:SG	oxidized, CA 50.338, CB 41.788 ppm	oxidized, CA 54.181, CB 39.17 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34531_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1076		99.0 (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: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 596
  - ¹³C chemical shifts: 373
  - ¹⁵N chemical shifts: 107
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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, Lypd6b, NEUROPEPTIDE, nicotinic acetylcholine receptor modulator, three-finger proteins