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BMRB: 25031

2MQF

NMR structure of spider toxin Mu-TRTX-Hhn2b

Authors

Klint, J.K., Chin, Y.K.Y., Mobli, M.

Assembly

spider-venom peptides against the analgesics target NaV1

Entity

1. spider-venom peptides against the analgesics target NaV1 (polymer, Thiol state: all disulfide bound), 34 monomers, 3685.281 Da Detail

AECKGFGKSC VPGKNECCSG YACNSRDKWC KVLL

Formula weight

3685.281 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS18:SG
2	disulfide	sing	1:CYS10:SG	1:CYS23:SG
3	disulfide	sing	1:CYS17:SG	1:CYS30:SG

Source organism

Haplopelma hainanum

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.4 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.4 % (372 of 378)	99.0 % (197 of 199)	98.6 % (141 of 143)	94.4 % (34 of 36)
Backbone	97.0 % (196 of 202)	97.2 % (69 of 71)	98.0 % (96 of 98)	93.9 % (31 of 33)
Sidechain	100.0 % (206 of 206)	100.0 % (128 of 128)	100.0 % (75 of 75)	100.0 % (3 of 3)
Aromatic	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (14 of 14)	100.0 % (1 of 1)
Methyl	100.0 % (20 of 20)	100.0 % (10 of 10)	100.0 % (10 of 10)

1. entity

AECKGFGKSC VPGKNECCSG YACNSRDKWC KVLL

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 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: 2MQF, Strand ID: A Detail

Release date

2015-07-12

Citation

Rational Engineering Defines a Molecular Switch That Is Essential for Activity of Spider-Venom Peptides against the Analgesics Target NaV1.7
Klint, J.K., Chin, Y.K.Y., King, G.F., Mobli, M.
Mol. Pharmacol. (2015), 88, 1002-1010, PubMed 26429937 , DOI 10.1124/mol.115.100784 , Abstract

Related entities 1. spider-venom peptides against the analgesics target NaV1, : 1 : 4 : 126 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

3 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

4 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

6 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

9 4D HCC(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Hhn2b	[U-99% 13C; U-99% 15N]		300 mM
2	sodium acetate	natural abundance		20 mM
3	D2O	natural abundance		5 %
4	H2O	natural abundance		95 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25031_2mqf.nef
Input source #2: Coordindates	2mqf.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:3:CYS:SG	A:18:CYS:SG	oxidized, CA 54.752, CB 42.565 ppm	oxidized, CA 54.3, CB 41.5 ppm	1.998
A:10:CYS:SG	A:23:CYS:SG	oxidized, CA 53.233, CB 47.364 ppm	oxidized, CA 55.57, CB 42.52 ppm	2.092
A:17:CYS:SG	A:30:CYS:SG	oxidized, CA 55.489, CB 40.003 ppm	oxidized, CA 55.631, CB 40.015 ppm	2.057

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----
AECKGFGKSCVPGKNECCSGYACNSRDKWCKVLL
||||||||||||||||||||||||||||||||||
AECKGFGKSCVPGKNECCSGYACNSRDKWCKVLL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0

Content subtype: combined_25031_2mqf.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	372		100.0 (chain: A, length: 34)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	553 (1)	noe	97.1 (chain: A, length: 34)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	18 (1)	undefined	17.6 (chain: A, length: 34)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	306 (306)	.	97.1 (chain: A, length: 34)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	55 (55)	.	100.0 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 197
  - ¹³C chemical shifts: 140
  - ¹⁵N chemical shifts: 35
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 97.1%
- Total number of restraints: 553
- Weight of restraints: 1.0 (553)
- Potential type of restraints: upper-bound-parabolic (553)
- Range of distance target values: 2.53, 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
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 17.6%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: upper-bound-parabolic (18)
  - Range of distance target values: 1.98, 3.5 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 97.1%
- Total number of restraints: 306
- Total number of restraints per polymer type: 306
- Weight of restraints: 1.0 (306)
- Potential type of restraints: square-well-parabolic (306)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: DYANA/DIANA_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
  - Total number of restraints: 55
  - Total number of restraints per polymer type: 55
  - Weight of restraints: 1.0 (55)
  - Potential type of restraints: square-well-parabolic (55)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords NaV1.7, Spider toxin, Voltage gated ion channel, peptide