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BMRB: 19460

2MD0

Solution structure of ShK-like immunomodulatory peptide from Ancylostoma caninum (hookworm)

Authors

Chhabra, S., Swarbrick, J.D., Mohanty, B., Chang, S., Chandy, G.K., Pennington, M.W., Norton, R.S.

Assembly

ShK-like immunomodulatory peptide from Ancylostoma caninum

Entity

1. ShK-like immunomodulatory peptide from Ancylostoma caninum (polymer, Thiol state: all disulfide bound), 51 monomers, 5851.415 Da Detail

NDIRTAADME HCADEKNFDC RRSLRNGDCD NDDKLLEMGY YCPVTCGFCE P

Formula weight

5851.415 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS12:SG	1:CYS49:SG
2	disulfide	sing	1:CYS20:SG	1:CYS42:SG
3	disulfide	sing	1:CYS29:SG	1:CYS46:SG

Source organism

Ancylostoma caninum

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.7 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.7 % (521 of 556)	93.8 % (273 of 291)	92.5 % (196 of 212)	98.1 % (52 of 53)
Backbone	96.7 % (292 of 302)	96.1 % (99 of 103)	96.7 % (145 of 150)	98.0 % (48 of 49)
Sidechain	91.4 % (276 of 302)	92.6 % (174 of 188)	89.1 % (98 of 110)	100.0 % (4 of 4)
Aromatic	80.0 % (32 of 40)	100.0 % (20 of 20)	60.0 % (12 of 20)
Methyl	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (15 of 15)

1. ShK-like peptide Ac

NDIRTAADME HCADEKNFDC RRSLRNGDCD NDDKLLEMGY YCPVTCGFCE P

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.13 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 2MD0, Strand ID: A Detail

Release date

2014-06-29

Citation

Kv1.3 channel-blocking immunomodulatory peptides from parasitic worms: implications for autoimmune diseases
chhabra, S., Chang, S., Nguyen, H.M., Huq, R., Tanner, M.R., Londono, L.M., Estrada, R., Dhawan, V., Chauhan, S., Upadhyay, S.K., Figueros, M., Mohanty, B., Swarbrick, J.D., Wulff, H., Iadonato, S.P., Gutman, G.A., Beeton, C., Pennington, M.W., Norton, R.S., Chandy, G.K.
FASEB J. (2014), 28, 3952-3964, PubMed 24891519 , DOI 10.1096/fj.14-251967 , Abstract

Related entities 1. ShK-like immunomodulatory peptide from Ancylostoma caninum, : 1 : 5 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.4

#	Name	Isotope labeling	Type	Concentration
1	ShK-like_peptide_Ac	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19460_2md0.nef
Input source #2: Coordindates	2md0.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:12:CYS:SG	A:49:CYS:SG	oxidized, CA 55.284, CB 41.28 ppm	oxidized, CA 53.634, CB 45.018 ppm	2.019
A:20:CYS:SG	A:42:CYS:SG	oxidized, CA 57.204, CB 38.893 ppm	oxidized, CA 52.18, CB 42.06 ppm	2.017
A:29:CYS:SG	A:46:CYS:SG	oxidized 83.9%, reduced 16.1%, CA 54.702, CB 33.48 ppm	oxidized 86.3%, reduced 13.7%, CA 51.191, CB 33.122 ppm	2.021

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

--------10--------20--------30--------40--------50-
NDIRTAADMEHCADEKNFDCRRSLRNGDCDNDDKLLEMGYYCPVTCGFCEP
|||||||||||||||||||||||||||||||||||||||||||||||||||
NDIRTAADMEHCADEKNFDCRRSLRNGDCDNDDKLLEMGYYCPVTCGFCEP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	51	0	0	100.0

Content subtype: combined_19460_2md0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	527		100.0 (chain: A, length: 51)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1877 (1)	noe	98.0 (chain: A, length: 51)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	59 (59)	.	80.4 (chain: A, length: 51)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 275
  - ¹³C chemical shifts: 196
  - ¹⁵N chemical shifts: 56
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 98.0%
- Total number of restraints: 1868
- Weight of restraints: 1.0 (1868)
- Potential type of restraints: square-well-parabolic (1868)
- Range of distance target values: 1.95, 3.9 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 80.4%
- Total number of restraints: 59
- Total number of restraints per polymer type: 59
- Weight of restraints: 1.0 (59)
- Potential type of restraints: square-well-parabolic (59)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords hookworm, Kv1.3, ShK-like peptide