BMRBj - BMREntryMaster

Found 1 Document (1.366 seconds)

BMRB: 6857

2LUG

Solution structure of an immunodominant epitope of myelin basic protein (MBP) - Conformational dependence on environment of an intrinsically unstructured protein

Authors

Fares, C., Libich, D.S., Harauz, G.

Assembly

FF2 immunodominant peptide

Entity

1. FF2 immunodominant peptide (polymer, Thiol state: not present), 18 monomers, 2141.381 Da Detail

QDENPVVHFF KNIVTPRT

Formula weight

2141.381 Da

Source organism

Mus musculus

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 82.9 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	82.9 % (170 of 205)	86.3 % (101 of 117)	78.4 % (69 of 88)
Backbone	80.7 % (71 of 88)	97.1 % (33 of 34)	70.4 % (38 of 54)
Sidechain	86.7 % (117 of 135)	81.9 % (68 of 83)	94.2 % (49 of 52)
Aromatic	83.3 % (20 of 24)	83.3 % (10 of 12)	83.3 % (10 of 12)
Methyl	95.0 % (19 of 20)	100.0 % (10 of 10)	90.0 % (9 of 10)

1. FF2

QDENPVVHFF KNIVTPRT

Show sample condition

Sample

Temperature 298 (±0.1) K, pH 6.5 (±0.1), Details FF2 in aqueous solution

#	Name	Isotope labeling	Type	Concentration
1	FF2	no	protein	2 mM
2	KCl	no	salt	100 mM

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 74.9 %, Completeness (bb): 73.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	74.9 % (307 of 410)	91.0 % (213 of 234)	53.4 % (94 of 176)
Backbone	73.3 % (129 of 176)	98.5 % (67 of 68)	57.4 % (62 of 108)
Sidechain	73.7 % (199 of 270)	88.0 % (146 of 166)	51.0 % (53 of 104)
Aromatic	60.4 % (29 of 48)	79.2 % (19 of 24)	41.7 % (10 of 24)
Methyl	72.5 % (29 of 40)	100.0 % (20 of 20)	45.0 % (9 of 20)

1. FF2

QDENPVVHFF KNIVTPRT

Show sample condition

Sample

Temperature 300 (±0.1) K, pH 6.5 (±0.1), Details FF2 in organic solution

#	Name	Isotope labeling	Type	Concentration
3	FF2		protein	5 mM
4	TFE	[U-2H]	solvent	30 %

Chem. Shift Complete3

Sequence coverage: 100.0 %, Completeness: 68.9 %, Completeness (bb): 64.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	68.9 % (424 of 615)	91.7 % (322 of 351)	38.6 % (102 of 264)
Backbone	64.0 % (169 of 264)	99.0 % (101 of 102)	42.0 % (68 of 162)
Sidechain	68.6 % (278 of 405)	88.8 % (221 of 249)	36.5 % (57 of 156)
Aromatic	56.9 % (41 of 72)	80.6 % (29 of 36)	33.3 % (12 of 36)
Methyl	65.0 % (39 of 60)	100.0 % (30 of 30)	30.0 % (9 of 30)

1. FF2

QDENPVVHFF KNIVTPRT

Show sample condition

Sample

Temperature 318 (±0.1) K, pH 6.5 (±0.1), Details FF2 in aqueous solution

#	Name	Isotope labeling	Type	Concentration
1	FF2	no	protein	2 mM
2	KCl	no	salt	100 mM

Release date

2006-04-19

Citation

Solution NMR structure of an immunodominant epitope of myelin basic protein. Conformational dependence on environment of an intrinsically unstructured protein
Fares, C., Libich, D.S., Harauz, G.
FEBS J. (2006), 273, 601-614, PubMed 16420483 , DOI 10.1111/j.1742-4658.2005.05093.x , Abstract

Related entities 1. FF2 immunodominant peptide, : 1 : 11 : 5 : 6 entities Detail

Interaction partners 1. FF2 immunodominant peptide, : 36 interactors Detail

More details for 36 interactors identified by 9 citations

Experiments performed 3 experiments Detail

#	Name	Isotope labeling	Type	Concentration
5	FF2		protein	1 mM
6	DPC	[U-2H]	lipid	100 mM

#	Name	Isotope labeling	Type	Concentration
5	FF2		protein	1 mM
6	DPC	[U-2H]	lipid	100 mM

#	Name	Isotope labeling	Type	Concentration
5	FF2		protein	1 mM
6	DPC	[U-2H]	lipid	100 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6857_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr6857_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	190	100.0 (chain: 1, length: 18)
2	Assigned chemical shifts	chem_shift_list_2	Warning	155	100.0 (chain: 1, length: 18)
3	Assigned chemical shifts	chem_shift_list_3	OK	130	100.0 (chain: 1, length: 18)
1	Chemical shift references	chemical_shift_referencing	OK	2	No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 124
  - ¹³C chemical shifts: 66
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: 1
Saveframe: chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 137
  - ¹³C chemical shifts: 18
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1
Saveframe: chem_shift_list_3
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 130
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	HIS	HD1	8.474
11	LYS	HZ1	7.582
11	LYS	HZ2	7.582
11	LYS	HZ3	7.582

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	100	85.5
¹³C chemical shifts	88	66	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	33	97.1
¹³C chemical shifts	36	18	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	67	80.7
¹³C chemical shifts	52	48	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	8	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	10	83.3
¹³C chemical shifts	12	10	83.3

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	HIS	HD1	7.471
8	HIS	HE2	8.524
11	LYS	HZ1	7.823
11	LYS	HZ2	7.823
11	LYS	HZ3	7.823

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	112	95.7
¹³C chemical shifts	88	18	20.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	34	100.0
¹³C chemical shifts	36	18	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	78	94.0
¹³C chemical shifts	52	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	9	75.0
¹³C chemical shifts	12	0	0.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	HIS	HD1	6.909

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	109	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	34	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	75	90.4

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	10	83.3

Keywords amphipathic helix, correlation spectroscopy, immunodominant epitope, multiple sclerosis, myelin basic protein, solution NMR, amphipatic helix

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 (1.366 seconds)

BMRB: 6857

Sample

Sample

Sample

Related entities 1. FF2 immunodominant peptide, : 1 : 11 : 5 : 6 entities Detail

Interaction partners 1. FF2 immunodominant peptide, : 36 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3

Chemical shift validation 5 contents Detail