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BMRB: 34078

5MOU

NMR spatial structure of alpha-mammal toxin BeM9

Authors

Mineev, K.S., Kuldushev, N.A., Berkut, A.A., Grishin, E.V., Vassilevski, A.A., Arseniev, A.S.

Assembly

Alpha-mammal toxin BeM9

Entity

1. Alpha-mammal toxin BeM9 (polymer), 66 monomers, 7343.278 Da Detail

ARDAYIAKPH NCVYECYNPK GSYCNDLCTE NGAESGYCQI LGKYGNACWC IQLPDNVPIR IPGKCH

Formula weight

7343.278 Da

Source organism

Mesobuthus eupeus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.8 %, Completeness (bb): 68.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.8 % (600 of 743)	97.2 % (377 of 388)	54.0 % (154 of 285)	98.6 % (69 of 70)
Backbone	68.4 % (264 of 386)	96.2 % (128 of 133)	39.6 % (76 of 192)	98.4 % (60 of 61)
Sidechain	94.5 % (394 of 417)	97.6 % (249 of 255)	88.9 % (136 of 153)	100.0 % (9 of 9)
Aromatic	80.9 % (55 of 68)	100.0 % (34 of 34)	60.6 % (20 of 33)	100.0 % (1 of 1)
Methyl	96.2 % (50 of 52)	96.2 % (25 of 26)	96.2 % (25 of 26)

1. entity 1

ARDAYIAKPH NCVYECYNPK GSYCNDLCTE NGAESGYCQI LGKYGNACWC IQLPDNVPIR IPGKCH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 5MOU, Strand ID: A Detail

Release date

2018-01-09

Citation

Refined structure of BeM9 reveals arginine hand, an overlooked structural motif in scorpion toxins affecting sodium channels
Kuldyushev, N.A., Mineev, K.S., Berkut, A.A., Peigneur, S., Arseniev, A.S., Tytgat, J., Grishin, E.V., Vassilevski, A.A.
Proteins (2018), 86, 1117-1122, PubMed 30007037 , DOI 10.1002/prot.25583 , Abstract

Related entities 1. Alpha-mammal toxin BeM9, : 1 : 1 : 155 entities Detail

Experiments performed 9 experiments Detail

1 NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

3 2D DQF-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

5 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

6 3D HNHB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

7 3D HNHA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

8 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

9 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 303 K, pH 3.5, Details 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Alpha-mammal toxin BeM9	[U-99% 15N]		1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34078_5mou.nef
Input source #2: Coordindates	5mou.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:65:CYS:SG	oxidized, CB 45.161 ppm	oxidized, CB 38.533 ppm	2.016
A:16:CYS:SG	A:38:CYS:SG	oxidized, CB 46.831 ppm	oxidized, CB 39.199 ppm	2.044
A:24:CYS:SG	A:48:CYS:SG	oxidized, CB 38.548 ppm	oxidized, CB 38.944 ppm	2.093
A:28:CYS:SG	A:50:CYS:SG	oxidized, CB 35.782 ppm	oxidized, CB 38.558 ppm	2.103

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--------60------
ARDAYIAKPHNCVYECYNPKGSYCNDLCTENGAESGYCQILGKYGNACWCIQLPDNVPIRIPGKCH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ARDAYIAKPHNCVYECYNPKGSYCNDLCTENGAESGYCQILGKYGNACWCIQLPDNVPIRIPGKCH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	66	0	0	100.0

Content subtype: combined_34078_5mou.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	609		100.0 (chain: A, length: 66)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	684 (1)	noe	100.0 (chain: A, length: 66)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	247 (244)	.	100.0 (chain: A, length: 66)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 387
  - ¹³C chemical shifts: 151
  - ¹⁵N chemical shifts: 71
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 100.0%
- Total number of restraints: 684
- Weight of restraints: 1.0 (684)
- Potential type of restraints: upper-bound-parabolic (684)
- Range of distance target values: 0.0, 4.92 (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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 100.0%
- Total number of restraints: 244
- Total number of restraints per polymer type: 244
- Weight of restraints: 1.0 (244)
- Potential type of restraints: square-well-parabolic (244)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PROTEIN, PROTEIN NEUROTOXIN