BMRBj - BMREntryMaster

Found 1 Document (5.392 seconds)

BMRB: 25659

2N3X

Solution Structure of TDP-43 Amyloidogenic Core Region

Authors

Jiang, L., Zhao, J., Zhou, C., Hu, H.

Assembly

TDP-43 Amyloidogenic Core Region

Entity

1. TDP-43 Amyloidogenic Core Region (polymer, Thiol state: not present), 50 monomers, 5207.792 Da Detail

MNFGAFSINP AMMAAAQAAL QSSWGMMGML ASQQNQSGPS GNNQNQGNMQ

Formula weight

5207.792 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.0 %, Completeness: 61.1 %, Completeness (bb): 87.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	61.1 % (331 of 542)	48.9 % (139 of 284)	74.7 % (145 of 194)	73.4 % (47 of 64)
Backbone	87.5 % (259 of 296)	81.7 % (85 of 104)	91.0 % (131 of 144)	89.6 % (43 of 48)
Sidechain	39.7 % (115 of 290)	30.0 % (54 of 180)	60.6 % (57 of 94)	25.0 % (4 of 16)
Aromatic	6.3 % (2 of 32)	6.3 % (1 of 16)	0.0 % (0 of 15)	100.0 % (1 of 1)
Methyl	71.4 % (20 of 28)	64.3 % (9 of 14)	78.6 % (11 of 14)

1. entity

MNFGAFSINP AMMAAAQAAL QSSWGMMGML ASQQNQSGPS GNNQNQGNMQ

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

LACS Plot; CA

Referencing offset: -2.99 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -2.99 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2N3X, Strand ID: A Detail

Release date

2016-04-17

Citation

Two mutations G335D and Q343R within the amyloidogenic core region of TDP-43 influence its aggregation and inclusion formation
Jiang, L., Zhao, J., Yin, X., He, W., Yang, H., Che, M., Hu, H.
Sci. Rep. (2016), 6, 23928-23928, PubMed 27030292 , DOI 10.1038/srep23928 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 25667 released on 2016-04-17
    Title Solution Structure of the G335D Mutant of TDP-43 Amyloidogenic Core Region
  BMRB: 25668 released on 2016-04-17
    Title Solution Structure of the Q343R Mutant of TDP-43 Amyloidogenic Core Region

Related entities 1. TDP-43 Amyloidogenic Core Region, : 1 : 10 : 1 : 2 : 10 entities Detail

Interaction partners 1. TDP-43 Amyloidogenic Core Region, : 74 interactors Detail

More details for 74 interactors identified by 29 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

2 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

5 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

6 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311 - 360)	[U-99% 13C; U-99% 15N]		600 uM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	D2O	[U-99% 2H]		8 v/v
5	sodium azide	natural abundance		0.02 v/v

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25659_2n3x.nef
Input source #2: Coordindates	2n3x.cif
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

Sequence alignments

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

-------320-------330-------340-------350-------360
MNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQ
||||||||||||||||||||||||||||||||||||||||||||||||||
MNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQ
--------10--------20--------30--------40--------50

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	50	0	0	100.0

Content subtype: combined_25659_2n3x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	327		96.0 (chain: A, length: 50)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	60 (1)	noe	54.0 (chain: A, length: 50)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 96.0%
- Total number of assignments
  - ¹H chemical shifts: 137
  - ¹³C chemical shifts: 144
  - ¹⁵N chemical shifts: 46
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 54.0%
- Total number of restraints: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: square-well-parabolic (60)
- Range of distance target values: 1.96, 15.87 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Amyloidogenic Core Region, TDP-43