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BMRB: 18897

4B1Q

NMR structure of the glycosylated conotoxin CcTx from Conus consors

Authors

Hocking, H.G., Gerwig, G.J., Favreau, P., Stocklin, R., Kamerling, J.P., Boelens, R.

Assembly

NMR structure of the glycosylated conotoxin CcTx from Conus consors

Entity

1. polysaccharide (polymer, Thiol state: not present), 5 monomers, 910.8229 Da
2. CONOTOXIN CCTX (polymer, Thiol state: all disulfide bound), 30 monomers, 3231.741 Da Detail

AXWLVPSQIT TCCGYNXGTM CXSCMCTNTC

Total weight

4142.564 Da

Max. entity weight

3231.741 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	2:CYS13:SG	2:CYS26:SG
2	disulfide	sing	2:CYS12:SG	2:CYS21:SG
3	disulfide	sing	2:CYS24:SG	2:CYS30:SG

Source organism

Conus consors

Exptl. method

solution NMR

Refine. method

CYANA AND CNS

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 77.1 %, Completeness: 84.6 %, Completeness (bb): 76.1 % Detail

Polymer type: polysaccharide(D) polypeptide(L)

	Total	¹H	¹³C
All	84.6 % (209 of 247)	93.5 % (130 of 139)	73.1 % (79 of 108)
Backbone	76.1 % (102 of 134)	94.5 % (52 of 55)	63.3 % (50 of 79)
Sidechain	94.9 % (131 of 138)	92.9 % (78 of 84)	98.1 % (53 of 54)
Aromatic	78.9 % (15 of 19)	60.0 % (6 of 10)	100.0 % (9 of 9)
Methyl	100.0 % (24 of 24)	100.0 % (12 of 12)	100.0 % (12 of 12)

2. CONOTOXIN CCTX

AXWLVPSQIT TCCGYNXGTM CXSCMCTNTC

Show sample condition

Sample

Solvent system 95 % H2O/ 5% D2O, Pressure 1 atm, Temperature 292.000 K, pH 3.000, Details 1.1 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE	[U-13C; U-15N]		1.1 mM
2	CONOTOXIN_CCTX	[U-13C; U-15N]		1.1 mM

Chem. Shift Complete2

Sequence coverage: 0.0 %, Completeness: 42.3 %, Completeness (bb): 38.1 % Detail

Polymer type: polysaccharide(D) polypeptide(L)

	Total	¹H	¹³C
All	42.3 % (209 of 494)	46.8 % (130 of 278)	36.6 % (79 of 216)
Backbone	38.1 % (102 of 268)	47.3 % (52 of 110)	31.6 % (50 of 158)
Sidechain	47.5 % (131 of 276)	46.4 % (78 of 168)	49.1 % (53 of 108)
Aromatic	39.5 % (15 of 38)	30.0 % (6 of 20)	50.0 % (9 of 18)
Methyl	50.0 % (24 of 48)	50.0 % (12 of 24)	50.0 % (12 of 24)

2. CONOTOXIN CCTX

AXWLVPSQIT TCCGYNXGTM CXSCMCTNTC

Show sample condition

Sample

Solvent system 95 % H2O/ 5% D2O, Pressure 1 atm, Temperature 292.000 K, pH 3.000, Details 1.1 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE	[U-13C; U-15N]		1.1 mM
2	CONOTOXIN_CCTX	[U-13C; U-15N]		1.1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 4B1Q, Strand ID: P Detail

Release date

2013-01-28

Citation

Structure of the O-glycosylated conopeptide CcTx from Conus consors venom
Hocking, H.G., Gerwig, G.J., Dutertre, S., Violette, A., Favreau, P., Stocklin, R., Kamerling, J.P., Boelens, R.
Chemistry (2013), 19, 870-879, PubMed 23281027 , DOI 10.1002/chem.201202713 , Abstract

Related entities 2. CONOTOXIN CCTX, : 1 : 1 : 9 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18897_4b1q.nef
Input source #2: Coordindates	4b1q.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	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
P:12:CYS:SG	P:21:CYS:SG	oxidized, CA 53.896, CB 39.051 ppm	oxidized, CA 53.653, CB 46.949 ppm	2.027
P:13:CYS:SG	P:26:CYS:SG	oxidized, CA 55.112, CB 37.301 ppm	oxidized, CA 54.868, CB 35.656 ppm	2.029
P:24:CYS:SG	P:30:CYS:SG	oxidized, CA 57.164, CB 39.715 ppm	oxidized, CA 55.47, CB 40.392 ppm	2.026

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	Assigned chemical shifts, Coordinates
A	1	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Assigned chemical shifts, Coordinates
A	2	GAL	beta-D-galactopyranose	Assigned chemical shifts, Coordinates
A	3	GXL	alpha-L-galactopyranose	Assigned chemical shifts, Coordinates
A	4	NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	Coordinates
A	5	GXL	alpha-L-galactopyranose	Assigned chemical shifts
P	2	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Coordinates
P	17	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Coordinates
P	22	HYP	4-HYDROXYPROLINE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
P	P	30	0	0	100.0
A	A	5	1	0	100.0

Content subtype: combined_18897_4b1q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	253		100.0 (chain: P, length: 30)
2	Assigned chemical shifts	assigned_chem_shift_list_1_2	Warning	73		83.3 (chain: A, length: 6)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	622 (1)	noe	100.0 (chain: P, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: P, Chain length: 30, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 156
  - ¹³C chemical shifts: 97
- Completeness of assignments
  - Entity_assemble_ID: P
- 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: P
Saveframe: assigned_chem_shift_list_1_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 6, Sequence coverage: 83.3%
- Total number of assignments
  - ¹H chemical shifts: 44
  - ¹³C chemical shifts: 29
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	TRP	CD2	129.435
3	TRP	CE2	138.759
3	TRP	CG	111.038
15	TYR	CG	130.593

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	156	99.4
¹³C chemical shifts	123	93	75.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	57	98.3
¹³C chemical shifts	60	30	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	99	100.0
¹³C chemical shifts	63	63	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0
¹³C chemical shifts	14	14	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	9	9	100.0

Comp_index_ID	Comp_ID
0	NDG
2	GAL
3	GXL
4	NDG
5	GXL

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	9	100.0
¹³C chemical shifts	8	6	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0
¹³C chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1	1	100.0
¹³C chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: P, Chain length: 30, Sequence coverage: 100.0%
- Total number of restraints: 621
- Weight of restraints: 1.0 (621)
- Potential type of restraints: square-well-parabolic (621)
- Range of distance target values: 1.23, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: P
- Distance restraints on contact map

Keywords kappaA-conotoxin O-glycan core type 9, O-GLYCAN, TOXIN

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Found 1 Document (0.416 seconds)

BMRB: 18897

Sample

Sample

Related entities 2. CONOTOXIN CCTX, : 1 : 1 : 9 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail