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BMRB: 25151

2MT7

Solution structure of spider-venom peptide Hs1a

Authors

Klint, J.K., King, G.F., Mobli, M.

Assembly

Hs1a

Entity

1. Hs1a (polymer, Thiol state: all disulfide bound), 35 monomers, 3859.483 Da Detail

GNDCLGFWSA CNPKNDKCCA NLVCSSKHKW CKGKL

Formula weight

3859.483 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.3 %, Completeness (bb): 83.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.3 % (362 of 401)	98.6 % (208 of 211)	76.7 % (115 of 150)	97.5 % (39 of 40)
Backbone	83.2 % (173 of 208)	97.2 % (70 of 72)	68.6 % (70 of 102)	97.1 % (33 of 34)
Sidechain	98.2 % (221 of 225)	99.3 % (138 of 139)	96.2 % (77 of 80)	100.0 % (6 of 6)
Aromatic	94.7 % (36 of 38)	100.0 % (19 of 19)	88.2 % (15 of 17)	100.0 % (2 of 2)
Methyl	100.0 % (20 of 20)	100.0 % (10 of 10)	100.0 % (10 of 10)

1. Hs1a

GNDCLGFWSA CNPKNDKCCA NLVCSSKHKW CKGKL

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MT7, Strand ID: A Detail

Release date

2015-08-16

Citation

Nav1.7 inhibitors normalise mechanical responses in chronic visceral hypersensitivity
Klint, J.K., Castro, J., Vetter, I., Er, S.Y., Cardoso, F., Liu, Y., Hagan, R., Neff, R., Minassian, N., Huang, J.X., Cooper, M.A., Wickenden, A., Mobli, M., Jin, L., Nicolazzo, J.A., Lewis, R.J., Bosmans, F., Brierley, S.M., King, G.F.
Not known

Related entities 1. Hs1a, : 1 : 133 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

2 3D HNCO

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

4 3D HNCACB

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

8 4D HCC(CO)NH TOCSY

Instrument

Bruker Avance - 900 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details pH 4.9

#	Name	Isotope labeling	Type	Concentration
1	Hs1a	[U-98% 13C; U-98% 15N]		0.5 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25151_2mt7.nef
Input source #2: Coordindates	2mt7.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:4:CYS:SG	A:19:CYS:SG	oxidized, CA 54.434, CB 43.435 ppm	oxidized, CA 54.765, CB 41.641 ppm	2.102
A:11:CYS:SG	A:24:CYS:SG	oxidized, CA 54.064, CB 45.772 ppm	oxidized, CA 55.881, CB 38.345 ppm	1.998
A:18:CYS:SG	A:31:CYS:SG	oxidized, CA 56.883, CB 39.062 ppm	oxidized, CA 54.779, CB 39.558 ppm	2.018

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-----
GNDCLGFWSACNPKNDKCCANLVCSSKHKWCKGKL
|||||||||||||||||||||||||||||||||||
GNDCLGFWSACNPKNDKCCANLVCSSKHKWCKGKL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0

Content subtype: combined_25151_2mt7.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	358		100.0 (chain: A, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	842 (1)	noe	97.1 (chain: A, length: 35)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	51 (51)	.	97.1 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 208
  - ¹³C chemical shifts: 111
  - ¹⁵N chemical shifts: 39
- 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: 35, Sequence coverage: 97.1%
- Total number of restraints: 835
- Weight of restraints: 1.0 (835)
- Potential type of restraints: upper-bound-parabolic (835)
- Range of distance target values: 2.33, 5.5 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 97.1%
- Total number of restraints: 51
- Total number of restraints per polymer type: 51
- Weight of restraints: 1.0 (51)
- Potential type of restraints: square-well-parabolic (51)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Nav channel inhibitor, Nav1.7, inhibitor cystine knot, solution structure, spider-venom peptide