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BMRB: 34335

6Q5Z

H-Vc7.2, H-superfamily conotoxin

Authors

Nielsen, L.D., Foged, M.M., Teilum, K., Ellgaard, L.

Assembly

Conotoxin Vc7.2

Entity

1. Conotoxin Vc7.2 (polymer, Thiol state: all disulfide bound), 29 monomers, 3108.536 Da Detail

GAMGNVNCGG VPCKFGCCRE DRCREIDCD

Formula weight

3108.536 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS8:SG	1:CYS18:SG
2	disulfide	sing	1:CYS13:SG	1:CYS23:SG
3	disulfide	sing	1:CYS17:SG	1:CYS28:SG

Source organism

Conus victoriae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.6 %, Completeness: 76.2 %, Completeness (bb): 77.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.2 % (224 of 294)	86.5 % (134 of 155)	61.5 % (67 of 109)	76.7 % (23 of 30)
Backbone	77.3 % (133 of 172)	87.1 % (54 of 62)	70.7 % (58 of 82)	75.0 % (21 of 28)
Sidechain	70.5 % (103 of 146)	86.0 % (80 of 93)	41.2 % (21 of 51)	100.0 % (2 of 2)
Aromatic	50.0 % (5 of 10)	100.0 % (5 of 5)	0.0 % (0 of 5)
Methyl	100.0 % (14 of 14)	100.0 % (7 of 7)	100.0 % (7 of 7)

1. entity 1

GAMGNVNCGG VPCKFGCCRE DRCREIDCD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	H-Vc7.2	natural abundance		1 mM
2	Na-phosphate	natural abundance		25 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM [U-13C; U-15N] H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	H-Vc7.2	[U-13C; U-15N]		1 mM
4	Na-phosphate	natural abundance		25 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6Q5Z, Strand ID: A Detail

Release date

2019-04-07

Citation

The three-dimensional structure of an H-superfamily conotoxin reveals a granulin fold arising from a common ICK cysteine framework
Nielsen, L.D., Foged, M.M., Albert, A., Bertelsen, A.B., Soltoft, C.L., Robinson, S.D., Petersen, S.V., Purcell, A.W., Olivera, B.M., Norton, R.S., Vasskog, T., Safavi-Hemami, H., Teilum, K., Ellgaard, L.
J. Biol. Chem. (2019), 294, 8745-8759, PubMed 30975904 , DOI 10.1074/jbc.RA119.007491 , Abstract

Related entities 1. Conotoxin Vc7.2, : 1 : 1 : 9 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM [U-13C; U-15N] H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	H-Vc7.2	[U-13C; U-15N]		1 mM
4	Na-phosphate	natural abundance		25 mM

2 3D HNCA

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM [U-13C; U-15N] H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	H-Vc7.2	[U-13C; U-15N]		1 mM
4	Na-phosphate	natural abundance		25 mM

3 3D HN(CO)CA

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM [U-13C; U-15N] H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	H-Vc7.2	[U-13C; U-15N]		1 mM
4	Na-phosphate	natural abundance		25 mM

4 3D HNCO

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM [U-13C; U-15N] H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	H-Vc7.2	[U-13C; U-15N]		1 mM
4	Na-phosphate	natural abundance		25 mM

5 3D HN(CA)CO

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM [U-13C; U-15N] H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	H-Vc7.2	[U-13C; U-15N]		1 mM
4	Na-phosphate	natural abundance		25 mM

6 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM [U-13C; U-15N] H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	H-Vc7.2	[U-13C; U-15N]		1 mM
4	Na-phosphate	natural abundance		25 mM

7 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	H-Vc7.2	natural abundance		1 mM
2	Na-phosphate	natural abundance		25 mM

8 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.1, Details 1 mM H-Vc7.2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	H-Vc7.2	natural abundance		1 mM
2	Na-phosphate	natural abundance		25 mM

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_34335_6q5z.nef
Input source #2: Coordindates	6q5z.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)
A:8:CYS:SG	A:18:CYS:SG	unknown, CA 54.465 ppm	unknown, CA 55.084 ppm	2.021
A:13:CYS:SG	A:23:CYS:SG	unknown, CA 54.644 ppm	oxidized, CA 55.526, CB 39.081 ppm	2.023
A:17:CYS:SG	A:28:CYS:SG	unknown	unknown, CA 56.245 ppm	2.02

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---------
GAMGNVNCGGVPCKFGCCREDRCREIDCD
|||||||||||||||||||||||||||||
GAMGNVNCGGVPCKFGCCREDRCREIDCD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	29	0	0	100.0

Content subtype: combined_34335_6q5z.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	218		96.6 (chain: A, length: 29)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 96.6%
- Total number of assignments
  - ¹³C chemical shifts: 63
  - ¹H chemical shifts: 133
  - ¹⁵N chemical shifts: 22
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords Cysteine framework VI/VII, Cysteine rich, Mini-granulin fold, TOXIN