BMRBj - BMREntryMaster

Found 1 Document (5.879 seconds)

BMRB: 34737

7PY2

Structure of the low complexity domain of TDP-43 (fragment 309-350) with methionine sulfoxide modifications

Authors

Carrasco, J., Anton, R., Pantoja-Uceda, D., Laurents, D.V., Oroz, J.

Assembly

TAR DNA-binding protein 43

Entity

1. TAR DNA-binding protein 43 (polymer, Thiol state: not present), 42 monomers, 4331.800 Da Detail

GGXNFGAFSI NPAXXAAAQA ALQSSWGXXG XLASQQNQSG PS

Formula weight

4331.8 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 85.7 %, Completeness: 77.8 %, Completeness (bb): 92.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.8 % (284 of 365)	73.8 % (138 of 187)	81.5 % (110 of 135)	83.7 % (36 of 43)
Backbone	92.9 % (197 of 212)	89.5 % (68 of 76)	93.1 % (95 of 102)	100.0 % (34 of 34)
Sidechain	62.8 % (115 of 183)	63.1 % (70 of 111)	68.3 % (43 of 63)	22.2 % (2 of 9)
Aromatic	3.1 % (1 of 32)	6.3 % (1 of 16)	0.0 % (0 of 15)	0.0 % (0 of 1)
Methyl	89.3 % (25 of 28)	85.7 % (12 of 14)	92.9 % (13 of 14)

1. entity 1

GGXNFGAFSI NPAXXAAAQA ALQSSWGXXG XLASQQNQSG PS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 288 (±0.2) K, pH 6.8 (±0.05), Details 500 uM [U-13C; U-15N] TDP-43 fragment 309-350, 20 mM HEPES, 10 mM potassium chloride, 5 mM MgCl2, 1 mM ATP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

Release date

2022-06-26

Citation

Metamorphism in TDP-43 prion-like domain determines chaperone recognition
Carrasco, J., Anton, R., Valbuena, A., Pantoja-Uceda, D., Mukhi, M., Hervas, R., Laurents, D.V., Gasset, M., Oroz, J.
Nat. Commun. (2023), 14, 466-466, PubMed 36709343 , DOI 10.1038/s41467-023-36023-z , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 51494 released on 2022-06-15
Title Backbone 1H, 13C, and 15N Chemical Shift Assignments for TDP-43 low complexity domain with methionine sulfoxide modifications

Related entities 1. TAR DNA-binding protein 43, : 1 : 1 : 10 : 6 entities Detail

Interaction partners 1. TAR DNA-binding protein 43, : 74 interactors Detail

More details for 74 interactors identified by 29 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 288 (±0.2) K, pH 6.8 (±0.05), Details 500 uM [U-13C; U-15N] TDP-43 fragment 309-350, 20 mM HEPES, 10 mM potassium chloride, 5 mM MgCl2, 1 mM ATP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

2 3D HNCO

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

3 3D HN(CA)CO

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

4 3D HNCA

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

5 3D CBCA(CO)NH

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

6 3D HCC(CO)NH

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

7 3D HNNH

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

8 3D HNHA

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

9 3D 1H-15N NOESY

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TDP-43 fragment 309-350	[U-13C; U-15N]	500 uM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	10 mM
4	MgCl2	natural abundance	5 mM
5	ATP	natural abundance	1 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34737_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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	3	MHO	S-OXYMETHIONINE	Assigned chemical shifts
1	14	MHO	S-OXYMETHIONINE	Assigned chemical shifts
1	15	MHO	S-OXYMETHIONINE	Assigned chemical shifts
1	28	MHO	S-OXYMETHIONINE	Assigned chemical shifts
1	29	MHO	S-OXYMETHIONINE	Assigned chemical shifts
1	31	MHO	S-OXYMETHIONINE	Assigned chemical shifts

Content subtype: bmr34737_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	390		100.0 (chain: 1, length: 42)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 42, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 214
  - ¹³C chemical shifts: 136
  - ¹⁵N chemical shifts: 40
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID
3	MHO
14	MHO
15	MHO
28	MHO
29	MHO
31	MHO

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	187	148	79.1
¹³C chemical shifts	135	109	80.7
¹⁵N chemical shifts	43	34	79.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	75	98.7
¹³C chemical shifts	72	67	93.1
¹⁵N chemical shifts	34	34	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	111	73	65.8
¹³C chemical shifts	63	42	66.7
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	12	85.7
¹³C chemical shifts	14	12	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	1	6.2
¹³C chemical shifts	15	0	0.0
¹⁵N chemical shifts	1	0	0.0

Keywords LLPS, TDP-43, UNKNOWN FUNCTION, low complexity domain, methionine sulfoxide, prion-like domain

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Found 1 Document (5.879 seconds)

BMRB: 34737

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. TAR DNA-binding protein 43, : 1 : 1 : 10 : 6 entities Detail

Interaction partners 1. TAR DNA-binding protein 43, : 74 interactors Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 3 contents Detail