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BMRB: 18141

2LMZ

Solution NMR structure of the novel conotoxin im23a from Conus imperialis

Authors

Khoo, K.K., Galea, C.A., Boonyalai, N., Norton, R.S.

Assembly

novel conotoxin im23a from Conus imperialis

Entity

1. novel conotoxin im23a from Conus imperialis (polymer, Thiol state: all disulfide bound), 42 monomers, 4829.532 Da Detail

IPYCGQTGAE CYSWCIKQDL SKDWCCDFVK DIRMNPPADK CP

Formula weight

4829.532 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS11:SG
2	disulfide	sing	1:CYS15:SG	1:CYS25:SG
3	disulfide	sing	1:CYS26:SG	1:CYS41:SG

Source organism

Conus imperialis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 67.3 %, Completeness (bb): 61.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.3 % (330 of 490)	98.1 % (253 of 258)	18.0 % (34 of 189)	100.0 % (43 of 43)
Backbone	61.1 % (149 of 244)	98.8 % (81 of 82)	24.2 % (30 of 124)	100.0 % (38 of 38)
Sidechain	63.6 % (182 of 286)	97.7 % (172 of 176)	4.8 % (5 of 105)	100.0 % (5 of 5)
Aromatic	54.0 % (27 of 50)	100.0 % (25 of 25)	0.0 % (0 of 23)	100.0 % (2 of 2)
Methyl	61.5 % (16 of 26)	100.0 % (13 of 13)	23.1 % (3 of 13)

1. entity

IPYCGQTGAE CYSWCIKQDL SKDWCCDFVK DIRMNPPADK CP

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		128 uM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
4	entity	natural abundance		128 uM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

Protein Blocks Logo

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

Release date

2012-03-18

Citation

A helical conotoxin from Conus imperialis has a novel cysteine framework and defines a new superfamily
Ye, M., Khoo, K.K., Xu, S., Zhou, M., Boonyalai, N., Perugini, M.A., Shao, X., Chi, C., Galea, C.A., Wang, C., Norton, R.S.
J. Biol. Chem. (2012), 287, 14973-14983, PubMed 22399292 , DOI 10.1074/jbc.M111.334615 , Abstract

Related entities 1. novel conotoxin im23a from Conus imperialis, : 1 : 1 : 1 : 2 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		128 uM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		128 uM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

3 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		128 uM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

4 2D DQF-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		128 uM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		128 uM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

6 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		128 uM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

7 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
4	entity	natural abundance		128 uM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6

#	Name	Isotope labeling	Type	Concentration
4	entity	natural abundance		128 uM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18141_2lmz.nef
Input source #2: Coordindates	2lmz.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:11:CYS:SG	unknown, CA 53.5 ppm	unknown	2.02
A:15:CYS:SG	A:25:CYS:SG	unknown, CA 60.5 ppm	unknown	2.02
A:26:CYS:SG	A:41:CYS:SG	unknown, CA 58.9 ppm	unknown, CA 50.9 ppm	2.019

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--
IPYCGQTGAECYSWCIKQDLSKDWCCDFVKDIRMNPPADKCP
||||||||||||||||||||||||||||||||||||||||||
IPYCGQTGAECYSWCIKQDLSKDWCCDFVKDIRMNPPADKCP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	42	0	0	100.0

Content subtype: combined_18141_2lmz.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	325		100.0 (chain: A, length: 42)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	774 (1)	noe	100.0 (chain: A, length: 42)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	8 (1)	hbond	19.0 (chain: A, length: 42)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	50 (50)	.	81.0 (chain: A, length: 42)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 253
  - ¹³C chemical shifts: 29
  - ¹⁵N chemical shifts: 43
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 100.0%
- Total number of restraints: 774
- Weight of restraints: 1.0 (774)
- Potential type of restraints: square-well-parabolic (774)
- Range of distance target values: 2.29, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 19.0%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Range of distance target values: 2.1, 3.0 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 42, Sequence coverage: 81.0%
- Total number of restraints: 50
- Total number of restraints per polymer type: 50
- Weight of restraints: 1.0 (50)
- Potential type of restraints: square-well-parabolic (50)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords conotoxin, Conus imperialis, hairpin, helix, novel