BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BMRB Entry 30345

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30345
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry

Title: Solution structure of TDP-43 N-terminal domain dimer.   PubMed: 29438978

Deposition date: 2017-09-18 Original release date: 2018-02-21

Authors: Naik, M.; Wang, A.; Conicella, A.; Fawzi, N.

Citation: Wang, Ailin; Conicella, Alexander; Schmidt, Hermann Broder; Martin, Erik; Rhoads, Shannon; Reeb, Ashley; Nourse, Amanda; Ramirez Montero, Daniel; Ryan, Veronica; Rohatgi, Rajat; Shewmaker, Frank; Naik, Mandar; Mittag, Tanja; Ayala, Yuna; Fawzi, Nicolas. "A single N-terminal phosphomimic disrupts TDP-43 polymerization, phase separation and RNA splicing"  EMBO J. 37, e97452-e97452 (2018).

Assembly members:
entity_1, polymer, 83 residues, 9244.335 Da.
entity_2, polymer, 83 residues, 9196.318 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: GHMMSEYIRVTEDENDEPIE IPSEDDGTVLLSTVTAQFPG ACGLRYRNPVEQCMRGVRLV EGILHAPDAGWGNLVYVVNY PKD
entity_2: GHMMSERIRVTEDENDEPIE IPSEDDGTVLLSTVTAQFPG ACGLRYRNPVSQCMRGVRLV EGILHAPDAGWGNLVYVVNY PKD

Data sets:
Data typeCount
13C chemical shifts654
15N chemical shifts161
1H chemical shifts1080

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 83 residues - 9244.335 Da.

1   GLYHISMETMETSERGLUTYRILEARGVAL
2   THRGLUASPGLUASNASPGLUPROILEGLU
3   ILEPROSERGLUASPASPGLYTHRVALLEU
4   LEUSERTHRVALTHRALAGLNPHEPROGLY
5   ALACYSGLYLEUARGTYRARGASNPROVAL
6   GLUGLNCYSMETARGGLYVALARGLEUVAL
7   GLUGLYILELEUHISALAPROASPALAGLY
8   TRPGLYASNLEUVALTYRVALVALASNTYR
9   PROLYSASP

Entity 2, entity_2 83 residues - 9196.318 Da.

1   GLYHISMETMETSERGLUARGILEARGVAL
2   THRGLUASPGLUASNASPGLUPROILEGLU
3   ILEPROSERGLUASPASPGLYTHRVALLEU
4   LEUSERTHRVALTHRALAGLNPHEPROGLY
5   ALACYSGLYLEUARGTYRARGASNPROVAL
6   SERGLNCYSMETARGGLYVALARGLEUVAL
7   GLUGLYILELEUHISALAPROASPALAGLY
8   TRPGLYASNLEUVALTYRVALVALASNTYR
9   PROLYSASP

Samples:

sample_1: DTT 1 ± 0.01 mM; HEPES 20 ± 0.01 mM; TDP-43 NTD S48E, [U-99% 13C; U-99% 15N], 0.7 ± 0.01 mM; TDP-43 NTD Y4R 2.0 ± 0.01 mM

sample_2: DTT 1 ± 0.01 mM; HEPES 20 ± 0.01 mM; TDP-43 NTD S48E 2 ± 0.01 mM; TDP-43 NTD Y4R, [U-99% 13C; U-99% 15N], 0.7 ± 0.01 mM

sample_conditions_1: ionic strength: 0 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D Filtered 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
hbCBcgcdceHEsample_2isotropicsample_conditions_1
hbCBcgcdceHEsample_1isotropicsample_conditions_1
hbCBcgcdHDsample_2isotropicsample_conditions_1
hbCBcgcdHDsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D Filtered 1H-15N NOESYsample_1isotropicsample_conditions_1
3D Filtered 1H-13C NOESYsample_2isotropicsample_conditions_1
3D Filtered 1H-15N NOESYsample_2isotropicsample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.114, Goddard - chemical shift assignment, peak picking

TOPSPIN v3.5, Bruker Biospin - collection

X-PLOR NIH v2.45, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker Avance III HD 850 MHz
  • Bruker Avance II 500 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts