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BMRB: 25667

2N4G

Solution Structure of the G335D Mutant of TDP-43 Amyloidogenic Core Region

Authors

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

Assembly

G335D Mutant of TDP-43 Amyloidogenic Core Region

Entity

1. G335D Mutant of TDP-43 Amyloidogenic Core Region (polymer, Thiol state: not present), 50 monomers, 5265.828 Da Detail

MNFGAFSINP AMMAAAQAAL QSSWDMMGML ASQQNQSGPS GNNQNQGNMQ

Formula weight

5265.828 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.0 %, Completeness: 56.3 %, Completeness (bb): 78.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	56.3 % (306 of 544)	49.5 % (141 of 285)	61.0 % (119 of 195)	71.9 % (46 of 64)
Backbone	78.0 % (231 of 296)	83.5 % (86 of 103)	70.3 % (102 of 145)	89.6 % (43 of 48)
Sidechain	36.9 % (108 of 293)	30.2 % (55 of 182)	52.6 % (50 of 95)	18.8 % (3 of 16)
Aromatic	6.3 % (2 of 32)	6.3 % (1 of 16)	0.0 % (0 of 15)	100.0 % (1 of 1)
Methyl	75.0 % (21 of 28)	78.6 % (11 of 14)	71.4 % (10 of 14)

1. entity

MNFGAFSINP AMMAAAQAAL QSSWDMMGML ASQQNQSGPS GNNQNQGNMQ

Show sample condition

Sample

Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.3 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2N4G, 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

Related entities 1. G335D Mutant of TDP-43 Amyloidogenic Core Region, : 1 : 12 : 12 entities Detail

Interaction partners 1. G335D Mutant of 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 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

4 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

5 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

8 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	GB1-TDP(311-360)-G335D	[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 %
5	sodium azide	natural abundance		0.02 w/v
6	H2O	natural abundance		92 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25667_2n4g.nef
Input source #2: Coordindates	2n4g.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
MNFGAFSINPAMMAAAQAALQSSWDMMGMLASQQNQSGPSGNNQNQGNMQ
||||||||||||||||||||||||||||||||||||||||||||||||||
MNFGAFSINPAMMAAAQAALQSSWDMMGMLASQQNQSGPSGNNQNQGNMQ
--------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_25667_2n4g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	303		96.0 (chain: A, length: 50)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	74 (1)	noe	50.0 (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: 139
  - ¹⁵N chemical shifts: 46
  - ¹³C chemical shifts: 118
- 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: 50.0%
- Total number of restraints: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Range of distance target values: 1.64, 36.04 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Amyloidogenic Core Region, G335D, TDP-43