BMRBj - BMREntryMaster

	Total	¹H	¹³C
All	80.3 % (298 of 371)	96.7 % (207 of 214)	58.0 % (91 of 157)
Backbone	70.9 % (124 of 175)	95.9 % (70 of 73)	52.9 % (54 of 102)
Sidechain	89.9 % (205 of 228)	97.2 % (137 of 141)	78.2 % (68 of 87)
Aromatic	60.0 % (24 of 40)	100.0 % (21 of 21)	15.8 % (3 of 19)
Methyl	96.7 % (29 of 30)	100.0 % (15 of 15)	93.3 % (14 of 15)

1. Hm-3

GCIAKNKECA WFSGEWCCGA LSCKYSIKRN LKICV

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.2

#	Name	Isotope labeling	Concentration
1	hm3	natural abundance	0.5 mM
2	H20	natural abundance	95 %
3	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
4	Hm-3	natural abundance		0.5 mM
5	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2014-11-02

Citation

Structure of membrane-active toxin from crab spider Heriaeus melloteei suggests parallel evolution of sodium channel gating modifiers in Araneomorphae and Mygalomorphae
Berkut, A.A., Myshkin, M.YU., Peigneur, S., Paramonov, A.S., Lyukmanova, E.N., Tytgat, J., Arseniev, A.S., Grishin, E.V., Shenkarev, Z.O., Vassilevski, A.A.
J. Biol. Chem. (2015), 290, 492-504, PubMed 25352595 , DOI 10.1074/jbc.M114.595678 , Abstract

Related entities 1. membrane-active toxin from crab spider Heriaeus melloteei, : 1 : 1 : 5 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25050_2mqu.nef
Input source #2: Coordindates	2mqu.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:2:CYS:SG	A:18:CYS:SG	oxidized, CA 53.693, CB 42.729 ppm	oxidized, CB 40.878 ppm	2.055
A:9:CYS:SG	A:23:CYS:SG	oxidized, CA 53.222, CB 47.025 ppm	oxidized, CA 54.909, CB 39.453 ppm	1.91
A:17:CYS:SG	A:34:CYS:SG	oxidized, CA 54.656, CB 38.961 ppm	oxidized, CA 54.418, CB 39.191 ppm	1.905

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-----
GCIAKNKECAWFSGEWCCGALSCKYSIKRNLKICV
|||||||||||||||||||||||||||||||||||
GCIAKNKECAWFSGEWCCGALSCKYSIKRNLKICV

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_25050_2mqu.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	294		97.1 (chain: A, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	302 (1)	noe	97.1 (chain: A, length: 35)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	9 (1)	undefined	17.1 (chain: A, length: 35)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	9 (1)	undefined	17.1 (chain: A, length: 35)
4	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	26 (1)	hbond	57.1 (chain: A, length: 35)
5	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	26 (1)	hbond	57.1 (chain: A, length: 35)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_7	OK	85 (85)	.	100.0 (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: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 206
  - ¹³C chemical shifts: 88
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	214	206	96.3
¹³C chemical shifts	157	88	56.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	70	95.9
¹³C chemical shifts	70	20	28.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	141	136	96.5
¹³C chemical shifts	87	68	78.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	15	14	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0
¹³C chemical shifts	19	3	15.8

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 97.1%
- Total number of restraints: 302
- Weight of restraints: 1.0 (302)
- Potential type of restraints: upper-bound-parabolic (302)
- Range of distance target values: 0.0, 5.26 (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: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 17.1%
  - Total number of restraints: 9
  - Weight of restraints: 1.0 (9)
  - Potential type of restraints: upper-bound-parabolic (9)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 17.1%
    - Total number of restraints: 9
    - Weight of restraints: 1.0 (9)
    - Potential type of restraints: upper-bound-parabolic (9)
    - Range of distance target values: 2.0, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_3
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 57.1%
        --------10--------20--------30----- GCIAKNKECAWFSGEWCCGALSCKYSIKRNLKICV || || || | | | || | || |||||| ..IA.NK.CA..S..W.C..LS.K.SI..NLKICV
      - Total number of restraints: 26
        Total hydrogen bond restraints: 26
        O...H-x: 6
        O...h-N: 6
        Long range: 14
        O...H-x: 7
        O...h-N: 7
      - Weight of restraints: 1.0 (26)
        Total hydrogen bond restraints: 1.0 (26)
        O...H-x: 1.0 (6)
        O...h-N: 1.0 (6)
        Long range: 1.0 (14)
        O...H-x: 1.0 (7)
        O...h-N: 1.0 (7)
      - Potential type of restraints: upper-bound-parabolic (26)
        Total hydrogen bond restraints: upper-bound-parabolic (26)
        O...H-x: upper-bound-parabolic (6)
        O...h-N: upper-bound-parabolic (6)
        Long range: upper-bound-parabolic (14)
        O...H-x: upper-bound-parabolic (7)
        O...h-N: upper-bound-parabolic (7)
      - Range of distance target values: 2.3, 3.3 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
      - Saveframe: DYANA/DIANA_distance_constraints_5
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 57.1%
        --------10--------20--------30----- GCIAKNKECAWFSGEWCCGALSCKYSIKRNLKICV || || || | | | || | || |||||| ..IA.NK.CA..S..W.C..LS.K.SI..NLKICV
        Total number of restraints: 26
        Total hydrogen bond restraints: 26
        O...H-x (too close!): 6
        O...h-N (too close!): 6
        Long range: 14
        O...H-x (too close!): 7
        O...h-N (too close!): 7
        Weight of restraints: 1.0 (26)
        Total hydrogen bond restraints: 1.0 (26)
        O...H-x (too close!): 1.0 (6)
        O...h-N (too close!): 1.0 (6)
        Long range: 1.0 (14)
        O...H-x (too close!): 1.0 (7)
        O...h-N (too close!): 1.0 (7)
        Potential type of restraints: upper-bound-parabolic (26)
        Total hydrogen bond restraints: upper-bound-parabolic (26)
        O...H-x (too close!): upper-bound-parabolic (6)
        O...h-N (too close!): upper-bound-parabolic (6)
        Long range: upper-bound-parabolic (14)
        O...H-x (too close!): upper-bound-parabolic (7)
        O...h-N (too close!): upper-bound-parabolic (7)
        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
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
- Total number of restraints: 85
- Total number of restraints per polymer type: 85
- Weight of restraints: 1.0 (85)
- Potential type of restraints: square-well-parabolic (85)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords spider toxins, voltage-gated sodium channels, gating modifiers, inhibitor cystine knot, ICK, channel activation

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Found 1 Document (0.564 seconds)

BMRB: 25050

Sample #1

Sample #2

Related entities 1. membrane-active toxin from crab spider Heriaeus melloteei, : 1 : 1 : 5 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail