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BMRB: 25675

2N4P

SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF TDP-43

Authors

Mompean, M., Romano, V., Pantoja-Uceda, D., Stuani, C., Baralle, F., Buratti, E., Laurents, D.V.

Assembly

N-TERMINAL DOMAIN OF TDP-43

Entity

1. N-TERMINAL DOMAIN OF TDP-43 (polymer, Thiol state: all free), 89 monomers, 9841.832 Da Detail

MAGSHHHHHH GSMSEYIRVT EDENDEPIEI PSEDDGTVLL STVTAQFPGA CGLRYRNPVS QCMRGVRLVE GILHAPDAGW GNLVYVVNY

Formula weight

9841.832 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

ENERGY MINIMIZATION

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 93.2 %, Completeness (bb): 94.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (911 of 977)	94.4 % (473 of 501)	90.9 % (350 of 385)	96.7 % (88 of 91)
Backbone	94.1 % (493 of 524)	94.0 % (171 of 182)	93.4 % (241 of 258)	96.4 % (81 of 84)
Sidechain	93.1 % (496 of 533)	95.0 % (303 of 319)	89.9 % (186 of 207)	100.0 % (7 of 7)
Aromatic	85.4 % (70 of 82)	97.6 % (40 of 41)	72.5 % (29 of 40)	100.0 % (1 of 1)
Methyl	91.5 % (86 of 94)	91.5 % (43 of 47)	91.5 % (43 of 47)

1. entity

MAGSHHHHHH GSMSEYIRVT EDENDEPIEI PSEDDGTVLL STVTAQFPGA CGLRYRNPVS QCMRGVRLVE GILHAPDAGW GNLVYVVNY

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.51 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N4P, Strand ID: A Detail

Release date

2016-01-10

Citation

The TDP-43 N-terminal domain structure at high resolution
Mompean, M., Romano, V., Pantoja-Uceda, D., Stuani, C., Baralle, F., Buratti, E., Laurents, D.V.
FEBS J. (2016), 283, 1242-1260, PubMed 26756435 , DOI 10.1111/febs.13651 , Abstract

Related entities 1. N-TERMINAL DOMAIN OF TDP-43, : 5 : 10 entities Detail

Interaction partners 1. N-TERMINAL DOMAIN OF TDP-43, : 74 interactors Detail

More details for 74 interactors identified by 28 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

9 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

12 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.8

#	Name	Isotope labeling	Type	Concentration
1	NTD	[U-13C; U-15N]		0.6 mM
2	TCEP	natural abundance		0.0 ~ 0.0 mM
3	CD3COOD/CD3COO-Na+	natural abundance		0.0 ~ 0.0 mM
4	NaN3	natural abundance		0.0 ~ 0.0 mM
5	H20	natural abundance		90 %
6	D20	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25675_2n4p.nef
Input source #2: Coordindates	2n4p.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

--------10--------20--------30--------40--------50--------60--------70--------80---------
MAGSHHHHHHGSMSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNY
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAGSHHHHHHGSMSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	89	0	0	100.0

Content subtype: combined_25675_2n4p.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	925		97.8 (chain: A, length: 89)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1409 (1)	noe	93.3 (chain: A, length: 89)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	60 (60)	.	61.8 (chain: A, length: 89)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 481
  - ¹³C chemical shifts: 351
  - ¹⁵N chemical shifts: 93
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 93.3%
- Total number of restraints: 1409
- Weight of restraints: 1.0 (1409)
- Potential type of restraints: upper-bound-parabolic (1409)
- Range of distance target values: 2.43, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 61.8%
- Total number of restraints: 60
- Total number of restraints per polymer type: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: square-well-parabolic (60)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PROTEIN