BMRBj - BMREntryMaster

Found 1 Document (0.635 seconds)

BMRB: 34008

5LAH

NMR structure of the sea anemone peptide tau-AnmTx Ueq 12-1 with an uncommon fold

Authors

Mineev, K.S., Arseniev, A.S., Andreev, A.Y., Kozlov, S.A., Logashina, Y.A.

Assembly

tau-AnmTx Ueq 12-1

Entity

1. tau-AnmTx Ueq 12-1 (polymer, Thiol state: all disulfide bound), 45 monomers, 4802.207 Da Detail

CYPGQPGCGH CSRPNYCEGA RCESGFHDCG SDHWCDASGD RCCCA

Formula weight

4802.207 Da

Entity Connection

disulfide 5 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS1:SG	1:CYS8:SG
2	disulfide	sing	1:CYS11:SG	1:CYS42:SG
3	disulfide	sing	1:CYS17:SG	1:CYS35:SG
4	disulfide	sing	1:CYS22:SG	1:CYS43:SG
5	disulfide	sing	1:CYS29:SG	1:CYS44:SG

Source organism

Urticina eques

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.0 %, Completeness (bb): 76.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.0 % (366 of 441)	98.3 % (225 of 229)	59.3 % (99 of 167)	93.3 % (42 of 45)
Backbone	76.1 % (201 of 264)	98.9 % (93 of 94)	52.3 % (67 of 128)	97.6 % (41 of 42)
Sidechain	94.4 % (203 of 215)	97.8 % (132 of 135)	90.9 % (70 of 77)	33.3 % (1 of 3)
Aromatic	84.0 % (42 of 50)	96.0 % (24 of 25)	70.8 % (17 of 24)	100.0 % (1 of 1)
Methyl	100.0 % (6 of 6)	100.0 % (3 of 3)	100.0 % (3 of 3)

1. tau-AnmTx Ueq 12-1

CYPGQPGCGH CSRPNYCEGA RCESGFHDCG SDHWCDASGD RCCCA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium azide	natural abundance	1 mM
2	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 100% D2O

#	Name	Isotope labeling	Concentration
5	sodium azide	natural abundance	1 mM
6	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
7	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 10 models in PDB: 5LAH, Strand ID: A Detail

Release date

2016-11-10

Citation

New Disulfide-Stabilized Fold Provides Sea Anemone Peptide to Exhibit Both Antimicrobial and TRPA1 Potentiating Properties
Logashina, Y.A., Solstad, R.G., Mineev, K.S., Korolkova, Y.V., Mosharova, I.V., Dyachenko, I.A., Palikov, V.A., Palikova, Y.A., Murashev, A.N., Arseniev, A.S., Kozlov, S.A., Stensvag, K., Haug, T., Andreev, Y.A.
Toxins (Basel). (2017), 9, 154-154, PubMed 28468269 , DOI 10.3390/toxins9050154 , Abstract

Related entities 1. tau-AnmTx Ueq 12-1, : 13 entities Detail

Experiments performed 7 experiments Detail

1 NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium azide	natural abundance	1 mM
2	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium azide	natural abundance	1 mM
2	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium azide	natural abundance	1 mM
2	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 100% D2O

#	Name	Isotope labeling	Concentration
5	sodium azide	natural abundance	1 mM
6	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
7	D2O	natural abundance	100 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 100% D2O

#	Name	Isotope labeling	Concentration
5	sodium azide	natural abundance	1 mM
6	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
7	D2O	natural abundance	100 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 100% D2O

#	Name	Isotope labeling	Concentration
5	sodium azide	natural abundance	1 mM
6	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
7	D2O	natural abundance	100 %

7 2D DQF-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.05) K, pH 3.2 (±0.1), Details 0.5 mM tau-AnmTx Ueq 12-1, 1 mM sodium azide, 100% D2O

#	Name	Isotope labeling	Concentration
5	sodium azide	natural abundance	1 mM
6	tau-AnmTx Ueq 12-1	natural abundance	0.5 (±0.1) mM
7	D2O	natural abundance	100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34008_5lah.nef
Input source #2: Coordindates	5lah.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:1:CYS:SG	A:8:CYS:SG	oxidized, CB 39.151 ppm	oxidized, CB 40.1 ppm	1.968
A:11:CYS:SG	A:42:CYS:SG	oxidized, CA 56.614, CB 39.495 ppm	oxidized, CA 54.901, CB 39.257 ppm	2.122
A:17:CYS:SG	A:35:CYS:SG	oxidized, CB 44.309 ppm	oxidized, CB 46.598 ppm	2.118
A:22:CYS:SG	A:43:CYS:SG	oxidized, CB 37.152 ppm	oxidized, CB 41.559 ppm	1.996
A:29:CYS:SG	A:44:CYS:SG	oxidized, CA 53.201, CB 40.46 ppm	oxidized, CA 57.294, CB 38.159 ppm	1.997

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--------40-----
CYPGQPGCGHCSRPNYCEGARCESGFHDCGSDHWCDASGDRCCCA
|||||||||||||||||||||||||||||||||||||||||||||
CYPGQPGCGHCSRPNYCEGARCESGFHDCGSDHWCDASGDRCCCA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	45	0	0	100.0

Content subtype: combined_34008_5lah.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_chemical_shifts_1	Warning	371		100.0 (chain: A, length: 45)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	342 (1)	noe	100.0 (chain: A, length: 45)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	15 (1)	noe	22.2 (chain: A, length: 45)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	56 (1)	hbond	55.6 (chain: A, length: 45)
4	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	56 (1)	hbond	55.6 (chain: A, length: 45)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	132 (131)	.	100.0 (chain: A, length: 45)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 227
  - ¹³C chemical shifts: 99
  - ¹⁵N chemical shifts: 45
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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)
41	ARG	HH11	6.656
41	ARG	HH12	6.656

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	229	225	98.3
¹³C chemical shifts	167	99	59.3
¹⁵N chemical shifts	48	45	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	93	98.9
¹³C chemical shifts	90	29	32.2
¹⁵N chemical shifts	42	41	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	135	132	97.8
¹³C chemical shifts	77	70	90.9
¹⁵N chemical shifts	6	4	66.7

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	24	96.0
¹³C chemical shifts	24	17	70.8
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 100.0%
- Total number of restraints: 342
- Weight of restraints: 1.0 (342)
- Potential type of restraints: upper-bound-parabolic (342)
- Range of distance target values: 0.0, 4.95 (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_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 22.2%
  - Total number of restraints: 15
  - Weight of restraints: 1.0 (15)
  - Potential type of restraints: upper-bound-parabolic (15)
  - 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: 45, Sequence coverage: 55.6%
    - Total number of restraints: 56
    - Weight of restraints: 1.0 (56)
    - Potential type of restraints: upper-bound-parabolic (56)
    - Range of distance target values: 2.0, 3.4 (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: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 55.6%
        --------10--------20--------30--------40----- CYPGQPGCGHCSRPNYCEGARCESGFHDCGSDHWCDASGDRCCCA | | || | ||| | | || || |||| | |||||| .Y..Q..CG..S.PNY.E....E..FH.CG.DHWC.A..DRCCCA
      - Total number of restraints: 56
        Medium range restraints, 1 < | i - j | < 5 : 6
        Backbone-backbone: 6
        Long range restraints, | i - j | >= 5 : 12
        Total hydrogen bond restraints: 38
        O...H-x (too close!): 8
        O...h-N (too close!): 8
        Long range: 22
        O...H-x (too close!): 11
        O...h-N (too close!): 11
      - Weight of restraints: 1.0 (56)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (6)
        Backbone-backbone: 1.0 (6)
        Long range restraints, | i - j | >= 5 : 1.0 (12)
        Total hydrogen bond restraints: 1.0 (38)
        O...H-x (too close!): 1.0 (8)
        O...h-N (too close!): 1.0 (8)
        Long range: 1.0 (22)
        O...H-x (too close!): 1.0 (11)
        O...h-N (too close!): 1.0 (11)
      - Potential type of restraints: upper-bound-parabolic (56)
        Medium range restraints, 1 < | i - j | < 5 : upper-bound-parabolic (6)
        Backbone-backbone: upper-bound-parabolic (6)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (12)
        Total hydrogen bond restraints: upper-bound-parabolic (38)
        O...H-x (too close!): upper-bound-parabolic (8)
        O...h-N (too close!): upper-bound-parabolic (8)
        Long range: upper-bound-parabolic (22)
        O...H-x (too close!): upper-bound-parabolic (11)
        O...h-N (too close!): upper-bound-parabolic (11)
      - Range of distance target values: 1.7, 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_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 45, Sequence coverage: 100.0%
- Total number of restraints: 131
- Total number of restraints per polymer type: 131
- Weight of restraints: 1.0 (131)
- Potential type of restraints: square-well-parabolic (131)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PROTEIN, TRPA1 potentiator, antimicrobial peptide, membrane protein, sea anemone

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 (0.635 seconds)

BMRB: 34008

Sample #1

Sample #2

Related entities 1. tau-AnmTx Ueq 12-1, : 13 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail