Structural basis for the inhibition of voltage-gated sodium channels with conotoxin-muOxi-GVIIJ
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:CYS29:SG |
3 | disulfide | sing | 1:CYS17:SG | 1:CYS29:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 75.0 % (267 of 356) | 93.4 % (171 of 183) | 47.1 % (65 of 138) | 88.6 % (31 of 35) |
Backbone | 78.4 % (160 of 204) | 98.6 % (72 of 73) | 58.8 % (57 of 97) | 91.2 % (31 of 34) |
Sidechain | 72.9 % (132 of 181) | 90.0 % (99 of 110) | 47.1 % (33 of 70) | 0.0 % (0 of 1) |
Aromatic | 68.4 % (26 of 38) | 100.0 % (19 of 19) | 38.9 % (7 of 18) | 0.0 % (0 of 1) |
Methyl | 55.6 % (10 of 18) | 77.8 % (7 of 9) | 33.3 % (3 of 9) |
1. GVIIJ C24S
GWCGDXGATC GKLRLYCCSG FCDSYTKTCK DKSSASolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | GVIIJ_C24S | natural abundance | 1.4 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | GVIIJ_C24S | natural abundance | 1.4 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | GVIIJ_C24S | natural abundance | 1.4 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | GVIIJ_C24S | natural abundance | 1.4 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | GVIIJ_C24S | natural abundance | 1.4 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | GVIIJ_C24S | natural abundance | 1.4 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_26674_2n8h.nef |
Input source #2: Coordindates | 2n8h.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 | True (see coodinates for details) |
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 53.194, CB 42.423 ppm | oxidized, CA 56.187, CB 38.387 ppm | 2.031 |
A:10:CYS:SG | A:22:CYS:SG | oxidized, CA 54.034, CB 46.146 ppm | oxidized, CA 53.219, CB 39.353 ppm | 2.032 |
A:17:CYS:SG | A:29:CYS:SG | oxidized, CA 54.47, CB 36.672 ppm | oxidized, CA 53.937, CB 37.465 ppm | 2.029 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
1:5:ASP:C | 1:6:HYP:N | unknown | unknown | n/a |
1:6:HYP:C | 1:7:GLY:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
A | 6 | HYP | 4-HYDROXYPROLINE | Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates |
Sequence alignments
--------10--------20--------30----- GWCGDXGATCGKLRLYCCSGFCDSYTKTCKDKSSA ||||||||||||||||||||||||||||||||||| GWCGDXGATCGKLRLYCCSGFCDSYTKTCKDKSSA
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_26674_2n8h.nef
Assigned chemical shifts
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
12 | LYS | HZ1 | 7.54 |
12 | LYS | HZ2 | 7.54 |
12 | LYS | HZ3 | 7.54 |
27 | LYS | HZ1 | 7.477 |
27 | LYS | HZ2 | 7.477 |
27 | LYS | HZ3 | 7.477 |
30 | LYS | HZ1 | 7.597 |
30 | LYS | HZ2 | 7.597 |
30 | LYS | HZ3 | 7.597 |
32 | LYS | HZ1 | 7.464 |
32 | LYS | HZ2 | 7.464 |
32 | LYS | HZ3 | 7.464 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 189 | 174 | 92.1 |
13C chemical shifts | 143 | 63 | 44.1 |
15N chemical shifts | 36 | 31 | 86.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 74 | 73 | 98.6 |
13C chemical shifts | 70 | 32 | 45.7 |
15N chemical shifts | 34 | 31 | 91.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 115 | 101 | 87.8 |
13C chemical shifts | 73 | 31 | 42.5 |
15N chemical shifts | 2 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 9 | 7 | 77.8 |
13C chemical shifts | 9 | 3 | 33.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 19 | 19 | 100.0 |
13C chemical shifts | 18 | 3 | 16.7 |
15N chemical shifts | 1 | 0 | 0.0 |
Covalent bonds
Distance restraints
--------10--------20--------30----- GWCGDXGATCGKLRLYCCSGFCDSYTKTCKDKSSA ||||| ||| ||||| || |||||||||||| .WCGDX.ATC.KLRLY.CS.FCDSYTKTCKDK --------10--------20--------30--
Dihedral angle restraints
--------10--------20--------30----- GWCGDXGATCGKLRLYCCSGFCDSYTKTCKDKSSA |||||||||| ||||||||||||||||||| GWCGDXGATC...RLYCCSGFCDSYTKTCKDK --------10--------20--------30--