BMRBj - BMREntryMaster

Found 1 Document (0.589 seconds)

BMRB: 26674

2N8H

Structural basis for the inhibition of voltage-gated sodium channels with conotoxin-muOxi-GVIIJ

Authors

Green, B.R., Chhabra, S., Norton, R.S.

Assembly

GVIIJ[C24S]

Entity

1. GVIIJ[C24S] (polymer, Thiol state: all disulfide bound), 35 monomers, 3729.205 Da Detail

GWCGDXGATC GKLRLYCCSG FCDSYTKTCK DKSSA

Formula weight

3729.205 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS18:SG
2	disulfide	sing	1:CYS10:SG	1:CYS29:SG
3	disulfide	sing	1:CYS17:SG	1:CYS29:SG

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 75.0 %, Completeness (bb): 78.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.0 % (267 of 356)	93.4 % (171 of 183)	47.1 % (65 of 138)	88.6 % (31 of 35)
Backbone	78.4 % (160 of 204)	98.6 % (72 of 73)	58.8 % (57 of 97)	91.2 % (31 of 34)
Sidechain	72.9 % (132 of 181)	90.0 % (99 of 110)	47.1 % (33 of 70)	0.0 % (0 of 1)
Aromatic	68.4 % (26 of 38)	100.0 % (19 of 19)	38.9 % (7 of 18)	0.0 % (0 of 1)
Methyl	55.6 % (10 of 18)	77.8 % (7 of 9)	33.3 % (3 of 9)

1. GVIIJ C24S

GWCGDXGATC GKLRLYCCSG FCDSYTKTCK DKSSA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.2

#	Name	Isotope labeling	Concentration
1	GVIIJ_C24S	natural abundance	1.4 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N8H, Strand ID: A Detail

Release date

2016-01-31

Citation

Structural Basis for the Inhibition of Voltage-gated Sodium Channels by Conotoxin μO§-GVIIJ
Green, B.R., Gajewiak, J.R., Chhabra, S., Skalicky, J.J., Zhang, M., Bulaj, G., Olivera, B.M., Yoshikami, D., Norton, R.S.
J. Biol. Chem. (2016), 291, 7205-7220, PubMed 26817840 , DOI 10.1074/jbc.M115.697672 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26675 released on 2016-01-31
Title Structural basis for the inhibition of voltage-gated sodium channels with conotoxin-muOxi-GVIIJ

Related entities 1. GVIIJ[C24S], : 1 : 7 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_26674_2n8h.nef
Input source #2: Coordindates	2n8h.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:18:CYS:SG	oxidized, CA 53.194, CB 42.423 ppm	oxidized, CA 56.187, CB 38.387 ppm	2.031
A:10:CYS:SG	A:22:CYS:SG	oxidized, CA 54.034, CB 46.146 ppm	oxidized, CA 53.219, CB 39.353 ppm	2.032
A:17:CYS:SG	A:29:CYS:SG	oxidized, CA 54.47, CB 36.672 ppm	oxidized, CA 53.937, CB 37.465 ppm	2.029

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:ASP:C	1:6:HYP:N	unknown	unknown	n/a
1:6:HYP:C	1:7:GLY: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

Sequence alignments

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

--------10--------20--------30-----
GWCGDXGATCGKLRLYCCSGFCDSYTKTCKDKSSA
|||||||||||||||||||||||||||||||||||
GWCGDXGATCGKLRLYCCSGFCDSYTKTCKDKSSA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0

Content subtype: combined_26674_2n8h.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	282		100.0 (chain: A, length: 35)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	154 (1)	noe	77.1 (chain: A, length: 35)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	10 (1)	hbond	22.9 (chain: A, length: 35)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	48 (48)	.	82.9 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 188
  - ¹³C chemical shifts: 63
  - ¹⁵N chemical shifts: 31
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
12	LYS	HZ1	7.54
12	LYS	HZ2	7.54
12	LYS	HZ3	7.54
27	LYS	HZ1	7.477
27	LYS	HZ2	7.477
27	LYS	HZ3	7.477
30	LYS	HZ1	7.597
30	LYS	HZ2	7.597
30	LYS	HZ3	7.597
32	LYS	HZ1	7.464
32	LYS	HZ2	7.464
32	LYS	HZ3	7.464

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	174	92.1
¹³C chemical shifts	143	63	44.1
¹⁵N chemical shifts	36	31	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	73	98.6
¹³C chemical shifts	70	32	45.7
¹⁵N chemical shifts	34	31	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	115	101	87.8
¹³C chemical shifts	73	31	42.5
¹⁵N chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	7	77.8
¹³C chemical shifts	9	3	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	19	100.0
¹³C chemical shifts	18	3	16.7
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 77.1%
- Total number of restraints: 154
- Weight of restraints: 1.0 (154)
- Potential type of restraints: square-well-parabolic (154)
- Range of distance target values: 2.08, 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_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 22.9%
  - Total number of restraints: 10
  - Weight of restraints: 1.0 (10)
  - Potential type of restraints: square-well-parabolic (10)
  - Range of distance target values: 1.8, 2.7 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 82.9%
- Total number of restraints: 48
- Total number of restraints per polymer type: 48
- Weight of restraints: 1.0 (48)
- Potential type of restraints: square-well-parabolic (48)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.589 seconds)

BMRB: 26674

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. GVIIJ[C24S], : 1 : 7 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail