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Found 1 Document (0.412 seconds)

BMRB: 30519

6MJD

NMR Solution structure of GIIIC

Authors

Harvey, P.J., Durek, T., Craik, D.J.

Assembly

mu-Conotoxin GIIIC

Entity

1. mu-Conotoxin GIIIC (polymer, Thiol state: all disulfide bound), 23 monomers, 2599.154 Da Detail

RDCCTXXKKC KDRRCKXLKC CAX

Formula weight

2599.154 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS15:SG
2	disulfide	sing	1:CYS4:SG	1:CYS20:SG
3	disulfide	sing	1:CYS10:SG	1:CYS21:SG

Source organism

Conus geographus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 82.6 %, Completeness: 78.6 %, Completeness (bb): 79.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.6 % (176 of 224)	89.4 % (110 of 123)	61.0 % (50 of 82)	84.2 % (16 of 19)
Backbone	79.8 % (91 of 114)	97.4 % (37 of 38)	66.7 % (38 of 57)	84.2 % (16 of 19)
Sidechain	80.6 % (104 of 129)	85.9 % (73 of 85)	70.5 % (31 of 44)
Methyl	100.0 % (8 of 8)	100.0 % (4 of 4)	100.0 % (4 of 4)

1. entity 1

RDCCTXXKKC KDRRCKXLKC CAX

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5, Details 2.0 mM NA GIIIC, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GIIIC	natural abundance		2.0 (±0.1) mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5, Details 2.0 mM NA GIIIC, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	GIIIC	natural abundance		2.0 (±0.1) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6MJD, Strand ID: A Detail

Release date

2018-11-18

Citation

NMR Structure of μ-Conotoxin GIIIC: Leucine 18 Induces Local Repacking of the N-Terminus Resulting in Reduced Na_V Channel Potency
Harvey, P.J., Kurniawan, N.D., Finol-Urdaneta, R.K., McArthur, J.R., Van Lysebetten, D., Dash, T.S., Hill, J.M., Adams, D.J., Durek, T., Craik, D.J.
Molecules (2018), 23, E2715-E2715, PubMed 30360356 , DOI 10.3390/molecules23102715 , Abstract

Related entities 1. mu-Conotoxin GIIIC, : 1 : 1 : 7 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30519_6mjd.nef
Input source #2: Coordindates	6mjd.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:15:CYS:SG	oxidized, CA 59.245, CB 40.649 ppm	oxidized, CA 53.193, CB 37.303 ppm	2.027
A:4:CYS:SG	A:20:CYS:SG	oxidized, CA 53.15, CB 39.958 ppm	oxidized, CA 57.126, CB 43.128 ppm	2.029
A:10:CYS:SG	A:21:CYS:SG	oxidized, CA 55.76, CB 36.503 ppm	oxidized, CA 54.354, CB 38.875 ppm	2.02

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:THR:C	1:6:HYP:N	unknown	unknown	n/a
1:6:HYP:C	1:7:HYP:N	unknown	unknown	n/a
1:7:HYP:C	1:8:LYS:N	unknown	unknown	n/a
1:16:LYS:C	1:17:HYP:N	unknown	unknown	n/a
1:17:HYP:C	1:18:LEU:N	unknown	unknown	n/a
1:22:ALA:C	1:23:NH2: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
A	7	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	17	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Coordinates
A	23	NH2	AMINO GROUP	Distance restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20---
RDCCTXXKKCKDRRCKXLKCCAX
|||||||||||||||||||||||
RDCCTXXKKCKDRRCKXLKCCAX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	23	0	0	100.0

Content subtype: combined_30519_6mjd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	9		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	209		95.7 (chain: A, length: 23)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	234 (1)	noe	100.0 (chain: A, length: 23)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	6 (1)	hbond	26.1 (chain: A, length: 23)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	33 (33)	.	91.3 (chain: A, length: 23)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 134
  - ¹³C chemical shifts: 59
  - ¹⁵N chemical shifts: 16
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	LYS	HZ1	7.573
8	LYS	HZ2	7.573
8	LYS	HZ3	7.573
11	LYS	HZ1	7.526
11	LYS	HZ2	7.526
11	LYS	HZ3	7.526

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	143	128	89.5
¹³C chemical shifts	97	59	60.8
¹⁵N chemical shifts	23	16	69.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	40	97.6
¹³C chemical shifts	44	20	45.5
¹⁵N chemical shifts	20	16	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	102	88	86.3
¹³C chemical shifts	53	39	73.6
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 100.0%
- Total number of restraints: 234
- Weight of restraints: 1.0 (234)
- Potential type of restraints: square-well-parabolic (234)
- Range of distance target values: 2.33, 3.65 (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: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 23, Sequence coverage: 26.1%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 1.0, 1.5 (Å)
  - Histogram of 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: 23, Sequence coverage: 91.3%
- Total number of restraints: 33
- Total number of restraints per polymer type: 33
- Weight of restraints: 1.0 (33)
- Potential type of restraints: square-well-parabolic (33)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords TOXIN, conotoxin, sodium channel blocker

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Found 1 Document (0.412 seconds)

BMRB: 30519

Sample #1

Sample #2

Related entities 1. mu-Conotoxin GIIIC, : 1 : 1 : 7 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 5 contents Detail