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Found 1 Document (0.403 seconds)

BMRB: 30342

6AZA

NMR structure of sea anemone toxin Kappa-actitoxin-Ate1a

Authors

Chin, Y.K.-Y., Madio, B., King, G.F., Undheim, E.A.B.

Assembly

sea anemone toxin Kappa-actitoxin-Ate1a

Entity

1. sea anemone toxin Kappa-actitoxin-Ate1a (polymer), 18 monomers, 1892.284 Da Detail

RCKTCSKGRC RPKPNCGX

Formula weight

1892.284 Da

Source organism

Actinia tenebrosa

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 89.1 %, Completeness (bb): 79.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.1 % (171 of 192)	97.2 % (104 of 107)	76.8 % (53 of 69)	87.5 % (14 of 16)
Backbone	79.6 % (78 of 98)	94.1 % (32 of 34)	67.3 % (33 of 49)	86.7 % (13 of 15)
Sidechain	99.1 % (108 of 109)	98.6 % (72 of 73)	100.0 % (35 of 35)	100.0 % (1 of 1)
Methyl	100.0 % (2 of 2)	100.0 % (1 of 1)	100.0 % (1 of 1)

1. sea anemone toxin Kappa-actitoxin-Ate1a

RCKTCSKGRC RPKPNCGX

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 5 % D2O, 95 % H2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AteTx1	natural abundance	1 mM
2	D2O	natural abundance	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 100 % D2O, 100% D2O

#	Name	Isotope labeling	Concentration
5	AteTx1	natural abundance	1 mM
6	D2O	natural abundance	100 %
7	sodium phosphate	natural abundance	20 mM

Release date

2017-09-12

Citation

PHAB toxins: a unique family of predatory sea anemone toxins evolving via intra-gene concerted evolution defines a new peptide fold
Madio, B., Peigneur, S., Chin, Y., Hamilton, B.R., Henriques, S.T., Smith, J.J., Cristofori-Armstrong, B., Dekan, Z., Boughton, B.A., Alewood, P.F., Tytgat, J., King, G.F., Undheim, E.
Cell. Mol. Life Sci. (2018), 75, 4511-4524, PubMed 30109357 , DOI 10.1007/s00018-018-2897-6 , Abstract

Related entities 1. sea anemone toxin Kappa-actitoxin-Ate1a, : 1 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 5 % D2O, 95 % H2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AteTx1	natural abundance	1 mM
2	D2O	natural abundance	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 5 % D2O, 95 % H2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AteTx1	natural abundance	1 mM
2	D2O	natural abundance	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM

3 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 5 % D2O, 95 % H2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AteTx1	natural abundance	1 mM
2	D2O	natural abundance	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM

4 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 5 % D2O, 95 % H2O, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AteTx1	natural abundance	1 mM
2	D2O	natural abundance	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM

5 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 100 % D2O, 100% D2O

#	Name	Isotope labeling	Concentration
5	AteTx1	natural abundance	1 mM
6	D2O	natural abundance	100 %
7	sodium phosphate	natural abundance	20 mM

6 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6, Details 1 mM AteTx1, 20 mM sodium phosphate, 100 % D2O, 100% D2O

#	Name	Isotope labeling	Concentration
5	AteTx1	natural abundance	1 mM
6	D2O	natural abundance	100 %
7	sodium phosphate	natural abundance	20 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30342_6aza.nef
Input source #2: Coordindates	6aza.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:2:CYS:SG	A:16:CYS:SG	oxidized, CA 55.505, CB 40.615 ppm	oxidized, CA 53.632, CB 40.643 ppm	2.076
A:5:CYS:SG	A:10:CYS:SG	oxidized, CA 55.3, CB 45.223 ppm	oxidized, CA 55.015, CB 44.477 ppm	2.08

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)
1:17:GLY:C	1:18:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	18	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------
RCKTCSKGRCRPKPNCGX
||||||||||||||||||
RCKTCSKGRCRPKPNCGX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0

Content subtype: combined_30342_6aza.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_chemical_shifts_1	OK	175		100.0 (chain: A, length: 18)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	115 (1)	noe	88.9 (chain: A, length: 18)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	12 (1)	undefined	22.2 (chain: A, length: 18)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	147 (147)	.	88.9 (chain: A, length: 18)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	23 (23)	.	83.3 (chain: A, length: 18)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 106
  - ¹³C chemical shifts: 52
  - ¹⁵N chemical shifts: 17
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	106	97.2
¹³C chemical shifts	69	52	75.4
¹⁵N chemical shifts	20	17	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	32	94.1
¹³C chemical shifts	34	17	50.0
¹⁵N chemical shifts	16	14	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	74	98.7
¹³C chemical shifts	35	35	100.0
¹⁵N chemical shifts	4	3	75.0

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

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: 18, Sequence coverage: 88.9%
- Total number of restraints: 115
- Weight of restraints: 1.0 (115)
- Potential type of restraints: upper-bound-parabolic (115)
- Range of distance target values: 2.31, 5.5 (Å)
- Histogram of 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: 18, Sequence coverage: 22.2%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: upper-bound-parabolic (12)
  - Range of distance target values: 2.0, 3.1 (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: 18, Sequence coverage: 88.9%
- Total number of restraints: 147
- Total number of restraints per polymer type: 147
- Weight of restraints: 1.0 (147)
- Potential type of restraints: square-well-parabolic (147)
- 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: 18, Sequence coverage: 83.3%
  - Total number of restraints: 23
  - Total number of restraints per polymer type: 23
  - Weight of restraints: 1.0 (23)
  - Potential type of restraints: square-well-parabolic (23)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords Sea anemone; Actinia tenebrosa; Neurotoxin; Ion channels, TOXIN

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Found 1 Document (0.403 seconds)

BMRB: 30342

Sample #1

Sample #2

Related entities 1. sea anemone toxin Kappa-actitoxin-Ate1a, : 1 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail