BMRBj - BMREntryMaster

Found 1 Document (0.617 seconds)

BMRB: 34547

6ZZE

Structure of the trans-(Tyr39-Pro40) form of the Human Secreted Ly-6/uPAR Related Protein-1 (SLURP-1)

Authors

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

Assembly

Secreted Ly-6/uPAR-related protein 1

Entity

1. Secreted Ly-6/uPAR-related protein 1 (polymer, Thiol state: all disulfide bound), 82 monomers, 8984.293 Da Detail

MLKCYTCKEP MTSASCRTIT RCKPEDTACM TTLVTVEAEY PFNQSPVVTR SCSSSCVATD PDSIGAAHLI FCCFRDLCNS EL

Formula weight

8984.293 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS22:SG
2	disulfide	sing	1:CYS4:SG	1:CYS29:SG
3	disulfide	sing	1:CYS7:SG	1:CYS16:SG
4	disulfide	sing	1:CYS22:SG	1:CYS52:SG
5	disulfide	sing	1:CYS56:SG	1:CYS72:SG
6	disulfide	sing	1:CYS73:SG	1:CYS78:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.6 %, Completeness (bb): 95.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.6 % (826 of 892)	97.1 % (442 of 455)	85.6 % (302 of 353)	97.6 % (82 of 84)
Backbone	95.0 % (458 of 482)	100.0 % (160 of 160)	90.2 % (221 of 245)	100.0 % (77 of 77)
Sidechain	90.8 % (446 of 491)	95.6 % (282 of 295)	84.1 % (159 of 189)	71.4 % (5 of 7)
Aromatic	38.0 % (19 of 50)	68.0 % (17 of 25)	8.0 % (2 of 25)
Methyl	95.2 % (80 of 84)	100.0 % (42 of 42)	90.5 % (38 of 42)

1. entity 1

MLKCYTCKEP MTSASCRTIT RCKPEDTACM TTLVTVEAEY PFNQSPVVTR SCSSSCVATD PDSIGAAHLI FCCFRDLCNS EL

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	SLURP-1	[U-15N]		0.3 (±0.03) mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

Protein Blocks Logo

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

Release date

2020-08-31

Citation

Biochemical Basis of Skin Disease Mal de Meleda: SLURP-1 Mutants Differently Affect Keratinocyte Proliferation and Apoptosis
Shulepko, M.A., Bychkov, M.L., Shenkarev, Z.O., Kulbatskii, D.S., Makhonin, A.M., Paramonov, A.S., Chugunov, A.O., Kirpichnikov, M.P., Lyukmanova, E.N.
J. Invest. Dermatol. (2021), 141, 2229-2237, PubMed 33741389 , DOI 10.1016/j.jid.2021.01.035 , Abstract

Related entities 1. Secreted Ly-6/uPAR-related protein 1, : 1 : 1 : 2 : 49 entities Detail

Interaction partners 1. Secreted Ly-6/uPAR-related protein 1, : 3 interactors Detail

More details for 3 interactors identified by 3 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	SLURP-1	[U-15N]		0.3 (±0.03) mM

2 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	SLURP-1	[U-15N]		0.3 (±0.03) mM

3 3D HNCO

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

4 3D HNCA

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

5 3D HNCACB

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

6 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

7 3D HNHA

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	SLURP-1	[U-15N]		0.3 (±0.03) mM

8 3D 1H-15N TOCSY

Instrument

Bruker AVANCE - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	SLURP-1	[U-15N]		0.3 (±0.03) mM

9 3D HN(CO)CA

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

10 2D 1H-13C HSQC

Instrument

Bruker AVANCE - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 4.7 (±0.05), Details 0.3 mM [U-13C; U-15N] SLURP-1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
2	SLURP-1	[U-13C; U-15N]		0.3 (±0.03) mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34547_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	1:22:CYS:SG	oxidized, CA 48.998, CB 38.912 ppm	oxidized, CA 48.887, CB 33.669 ppm	n/a
1:4:CYS:SG	1:29:CYS:SG	oxidized, CA 48.998, CB 38.912 ppm	oxidized, CA 49.138, CB 33.728 ppm	n/a
1:7:CYS:SG	1:16:CYS:SG	oxidized, CA 54.234, CB 43.098 ppm	oxidized, CA 53.227, CB 41.064 ppm	n/a
1:22:CYS:SG	1:52:CYS:SG	oxidized, CA 48.887, CB 33.669 ppm	oxidized, CA 55.095, CB 42.021 ppm	n/a
1:56:CYS:SG	1:72:CYS:SG	oxidized, CA 55.638, CB 37.3 ppm	oxidized, CA 49.869, CB 42.371 ppm	n/a
1:73:CYS:SG	1:78:CYS:SG	oxidized, CA 51.892, CB 41.131 ppm	oxidized, CA 53.532, CB 41.582 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34547_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	911		100.0 (chain: 1, length: 82)
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: 82, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 529
  - ¹³C chemical shifts: 301
  - ¹⁵N chemical shifts: 81
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	455	441	96.9
¹³C chemical shifts	353	301	85.3
¹⁵N chemical shifts	84	81	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	160	159	99.4
¹³C chemical shifts	164	142	86.6
¹⁵N chemical shifts	77	76	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	295	282	95.6
¹³C chemical shifts	189	159	84.1
¹⁵N chemical shifts	7	5	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	44	97.8
¹³C chemical shifts	45	40	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	17	68.0
¹³C chemical shifts	25	2	8.0

Keywords Ly-6, Lynx, Lynx1, NEUROPEPTIDE, SLURP, nicotinic acetylcholine receptor, snake neurotoxin, three-finger protein

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Found 1 Document (0.617 seconds)

BMRB: 34547

Sample #1

Sample #2

Sample #3

Related entities 1. Secreted Ly-6/uPAR-related protein 1, : 1 : 1 : 2 : 49 entities Detail

Interaction partners 1. Secreted Ly-6/uPAR-related protein 1, : 3 interactors Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 3 contents Detail