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BMRB: 25887

2N99

Solution structure of the SLURP-2, a secreted isoform of Lynx1

Authors

Paramonov, A.S., Shenkarev, Z.O., Lyukmanova, E.N., Arseniev, A.S.

Assembly

SLURP-2, a secreted isoform of Lynx1

Entity

1. SLURP-2, a secreted isoform of Lynx1 (polymer), 76 monomers, 8154.350 Da Detail

MIWCHQCTGF GGCSHGSRCL RDSTHCVTTA TRVLSNTEDL PLVTKMCHIG CPDIPSLGLG PYVSIACCQT SLCNHD

Formula weight

8154.35 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.9 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.9 % (772 of 805)	97.6 % (400 of 410)	93.1 % (296 of 318)	98.7 % (76 of 77)
Backbone	96.2 % (431 of 448)	98.1 % (152 of 155)	94.1 % (208 of 221)	98.6 % (71 of 72)
Sidechain	96.0 % (409 of 426)	97.3 % (248 of 255)	94.0 % (156 of 166)	100.0 % (5 of 5)
Aromatic	78.0 % (39 of 50)	84.0 % (21 of 25)	70.8 % (17 of 24)	100.0 % (1 of 1)
Methyl	96.2 % (77 of 80)	95.0 % (38 of 40)	97.5 % (39 of 40)

1. SLURP-2

MIWCHQCTGF GGCSHGSRCL RDSTHCVTTA TRVLSNTEDL PLVTKMCHIG CPDIPSLGLG PYVSIACCQT SLCNHD

Show sample condition

Sample

Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.38 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.38 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.81 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N99, Strand ID: A Detail

Release date

2016-09-14

Citation

Secreted Isoform of Human Lynx1 (SLURP-2): Spatial Structure and Pharmacology of Interactions with Different Types of Acetylcholine Receptors
Lyukmanova, E.N., Shulepko, M.A., Shenkarev, Z.O., Bychkov, M.L., Paramonov, A.S., Chugunov, A.O., Kulbatskii, D.S., Arvaniti, M., Dolejsi, E., Schaer, T., Arseniev, A.S., Efremov, R.G., Thomsen, M.S., Dolezal, V., Bertrand, D., Dolgikh, D.A., Kirpichnikov, M.P.
Sci. Rep. (2016), 6, 30698-30698, PubMed 27485575 , DOI 10.1038/srep30698 , Abstract

Related entities 1. SLURP-2, a secreted isoform of Lynx1, : 1 : 2 : 22 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

8 3D HNHA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

11 3D 1H-15N TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

12 3D HNHB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O/5% dioxane-d6, Pressure 1 atm, Temperature 315 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	SLURP-2	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	dioxane-d6	natural abundance		5 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25887_2n99.nef
Input source #2: Coordindates	2n99.cif
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)
A:103:CYS:SG	A:125:CYS:SG	oxidized, CA 52.011, CB 41.944 ppm	oxidized, CA 52.172, CB 36.484 ppm	1.909
A:106:CYS:SG	A:112:CYS:SG	oxidized, CA 53.907, CB 40.639 ppm	oxidized, CA 56.123, CB 41.79 ppm	1.97
A:118:CYS:SG	A:146:CYS:SG	oxidized, CA 52.996, CB 39.297 ppm	oxidized, CA 56.669, CB 46.298 ppm	1.996
A:150:CYS:SG	A:166:CYS:SG	oxidized, CA 50.265, CB 38.752 ppm	oxidized, CA 53.119, CB 48.826 ppm	2.132
A:167:CYS:SG	A:172:CYS:SG	oxidized, CA 55.141, CB 45.463 ppm	oxidized, CA 57.81, CB 45.571 ppm	1.92

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

100-----110-------120-------130-------140-------150-------160-------170-----
MIWCHQCTGFGGCSHGSRCLRDSTHCVTTATRVLSNTEDLPLVTKMCHIGCPDIPSLGLGPYVSIACCQTSLCNHD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIWCHQCTGFGGCSHGSRCLRDSTHCVTTATRVLSNTEDLPLVTKMCHIGCPDIPSLGLGPYVSIACCQTSLCNHD
--------10--------20--------30--------40--------50--------60--------70------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_25887_2n99.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	782		100.0 (chain: A, length: 76)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	644 (1)	noe	100.0 (chain: A, length: 76)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	15 (1)	undefined	13.2 (chain: A, length: 76)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	15 (1)	undefined	13.2 (chain: A, length: 76)
4	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	34 (1)	hbond	28.9 (chain: A, length: 76)
5	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	36 (1)	hbond	30.3 (chain: A, length: 76)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_7	Warning	1275 (1273)	.	100.0 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 404
  - ¹³C chemical shifts: 300
  - ¹⁵N chemical shifts: 78
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of restraints: 644
- Weight of restraints: 1.0 (644)
- Potential type of restraints: upper-bound-parabolic (644)
- Range of distance target values: 0.0, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 13.2%
  - Total number of restraints: 15
  - Weight of restraints: 1.0 (15)
  - Potential type of restraints: upper-bound-parabolic (15)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 13.2%
    - Total number of restraints: 15
    - Weight of restraints: 1.0 (15)
    - Potential type of restraints: upper-bound-parabolic (15)
    - Range of distance target values: 2.0, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_3
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 28.9%
      - Total number of restraints: 34
        Total hydrogen bond restraints: 34
      - Weight of restraints: 1.0 (34)
        Total hydrogen bond restraints: 1.0 (34)
      - Potential type of restraints: upper-bound-parabolic (34)
        Total hydrogen bond restraints: upper-bound-parabolic (34)
      - Range of distance target values: 2.3, 3.3 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
      - Saveframe: DYANA/DIANA_distance_constraints_5
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 30.3%
        Total number of restraints: 36
        Total hydrogen bond restraints: 36
        Weight of restraints: 1.0 (36)
        Total hydrogen bond restraints: 1.0 (36)
        Potential type of restraints: upper-bound-parabolic (36)
        Total hydrogen bond restraints: upper-bound-parabolic (36)
        Range of distance target values: 1.8, 2.7 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_7
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of restraints: 1273
- Total number of restraints per polymer type: 1273
- Weight of restraints: 1.0 (1273)
- Potential type of restraints: square-well-parabolic (1273)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ly-6, Lynx, SLURP, SLURP-2, cell proliferation, epithelium, keratinocyte, muscarinic acetylcholine receptor, neuromodulator, nicotinic acetylcholine receptor, three-finger protein, uPAR