BMRB Entry 19290

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19290
MolProbity Validation Chart

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Title:
NMR structure of human TDP-43 tandem RRMs in complex with UG-rich RNA
Deposition date:
2013-06-07
Original release date:
2013-06-28
Authors:
Lukavsky, Peter; Daujotyte, D.; Tollervey, J.; Ule, J.; Stuani, C.; Buratti, E.; Baralle, F.; Damberger, F.; Allain, F.
Citation:

Citation: Lukavsky, Peter; Daujotyte, Dalia; Tollervey, James; Ule, Jernej; Stuani, Cristiana; Buratti, Emanuele; Baralle, Francisco; Damberger, Fred; Allain, Frederic H-T. "Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43."  Nat. Struct. Mol. Biol. 20, 1443-1449 (2013).
PubMed: 24240615

Assembly members:

Assembly members:
TAR_DNA-BINDING_PROTEIN_43, polymer, 174 residues, 19955.5578 Da.
5'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3', polymer, 12 residues, 3933.29822 Da.

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TAR_DNA-BINDING_PROTEIN_43: GSHMASKTSDLIVLGLPWKT TEQDLKEYFSTFGEVLMVQV KKDLKTGHSKGFGFVRFTEY ETQVKVMSQRHMIDGRWCDC KLPNSKQSQDEPLRSRKVFV GRCTEDMTEDELREFFSQYG DVMDVFIPKPFRAFAFVTFA DDQIAQSLCGEDLIIKGISV HISNAEPKHNSNRQ
5'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3': GUGUGAAUGAAU

Data sets:
Data typeCount
13C chemical shifts864
15N chemical shifts182
1H chemical shifts1327
31P chemical shifts11

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1TAR DNA-BINDING PROTEIN 431
25'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3'2

Entities:

Entity 1, TAR DNA-BINDING PROTEIN 43 174 residues - 19955.5578 Da.

1   GLYSERHISMETALASERLYSTHRSERASP
2   LEUILEVALLEUGLYLEUPROTRPLYSTHR
3   THRGLUGLNASPLEULYSGLUTYRPHESER
4   THRPHEGLYGLUVALLEUMETVALGLNVAL
5   LYSLYSASPLEULYSTHRGLYHISSERLYS
6   GLYPHEGLYPHEVALARGPHETHRGLUTYR
7   GLUTHRGLNVALLYSVALMETSERGLNARG
8   HISMETILEASPGLYARGTRPCYSASPCYS
9   LYSLEUPROASNSERLYSGLNSERGLNASP
10   GLUPROLEUARGSERARGLYSVALPHEVAL
11   GLYARGCYSTHRGLUASPMETTHRGLUASP
12   GLULEUARGGLUPHEPHESERGLNTYRGLY
13   ASPVALMETASPVALPHEILEPROLYSPRO
14   PHEARGALAPHEALAPHEVALTHRPHEALA
15   ASPASPGLNILEALAGLNSERLEUCYSGLY
16   GLUASPLEUILEILELYSGLYILESERVAL
17   HISILESERASNALAGLUPROLYSHISASN
18   SERASNARGGLN

Entity 2, 5'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3' 12 residues - 3933.29822 Da.

1   GUGUGAAUGA
2   AU

Samples:

sample_1: TAR DNA-BINDING PROTEIN 43, [U-13C; U-15N], 0.7 mM; 5'-R(*GP*UP*GP*UP*GP*AP*AP*UP*GP*AP*AP*UP)-3' 0.7 mM

sample_conditions_1: ionic strength: 50.000 mM; pH: 6.800; pressure: 1 atm; temperature: 298.000 K

Experiments:

NameSampleSample stateSample conditions
3D C13-edited NOESYsample_1solutionsample_conditions_1
3D N15-edited NOESYsample_1solutionsample_conditions_1
2D NOESYsample_1solutionsample_conditions_1
2D TOCSYsample_1solutionsample_conditions_1
3D HCCH TOCSYsample_1solutionsample_conditions_1

Software:

AMBER vany, Case et al - chemical shift assignment

AutoDep v4.3 - chemical shift assignment

CYANA vany - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 900 MHz

Related Database Links:

UNP TADBP_HUMAN
PDB
DBJ BAD96474 BAE87159 BAG35326 BAG58707 BAG61425
EMBL CAB43367 CAG38565 CAH92854 CAL37794
GB AAA70033 AAH71657 AAH95435 ABO32290 ABO32291
REF NP_001127597 NP_031401 XP_001102660 XP_002750326 XP_003274288
SP Q13148 Q5R5W2
AlphaFold Q96DJ0 Q13148 Q5R5W2

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks