BMRB

Biological Magnetic Resonance Data Bank


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BMRB Entry 52142

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52142

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Title: 1H, 15N and 13C chemical shift assignments for the D2 domain of the human DEAD-box RNA helicase DDX3X   PubMed: 38664397

Deposition date: 2023-09-19 Original release date: 2024-03-18

Authors: Toyama, Yuki; Shimada, Ichio

Citation: Toyama, Yuki; Shimada, Ichio. "NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity"  Nat. Commun. 15, 3303-3303 (2024).

Assembly members:
entity_1, polymer, 201 residues, Formula weight is not available

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-SUMO

Entity Sequences (FASTA):
entity_1: GGGSTSENITQKVVWVEESD KRSFLLDLLNATGKDSLTLV FVETKKGADSLEDFLYHEGY ACTSIHGDRSQRDREEALHQ FRSGKSPILVATAVAARGLD ISNVKHVINFDLPSDIEEYV HRIGRTGRVGNLGLATSFFN ERNINITKDLLDLLVEAKQE VPSWLENMAYEHHYKGSSRG RSKSSRFSGGFGARDYRQSS G

Data sets:
Data typeCount
13C chemical shifts565
15N chemical shifts189
1H chemical shifts219

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1D2 domain1

Entities:

Entity 1, D2 domain 201 residues - Formula weight is not available

The first two Gly residues were introduced to facilitate the cleavage of N-terminal His-SUMO tag.

1   GLYGLYGLYSERTHRSERGLUASNILETHR
2   GLNLYSVALVALTRPVALGLUGLUSERASP
3   LYSARGSERPHELEULEUASPLEULEUASN
4   ALATHRGLYLYSASPSERLEUTHRLEUVAL
5   PHEVALGLUTHRLYSLYSGLYALAASPSER
6   LEUGLUASPPHELEUTYRHISGLUGLYTYR
7   ALACYSTHRSERILEHISGLYASPARGSER
8   GLNARGASPARGGLUGLUALALEUHISGLN
9   PHEARGSERGLYLYSSERPROILELEUVAL
10   ALATHRALAVALALAALAARGGLYLEUASP
11   ILESERASNVALLYSHISVALILEASNPHE
12   ASPLEUPROSERASPILEGLUGLUTYRVAL
13   HISARGILEGLYARGTHRGLYARGVALGLY
14   ASNLEUGLYLEUALATHRSERPHEPHEASN
15   GLUARGASNILEASNILETHRLYSASPLEU
16   LEUASPLEULEUVALGLUALALYSGLNGLU
17   VALPROSERTRPLEUGLUASNMETALATYR
18   GLUHISHISTYRLYSGLYSERSERARGGLY
19   ARGSERLYSSERSERARGPHESERGLYGLY
20   PHEGLYALAARGASPTYRARGGLNSERSER
21   GLY

Samples:

sample_2: D2 domain, [U-2H, 13C, 15N; Iled1-13C1H3; Leud/Valg-13C1H3/12CD3], 520 uM; MES 20 mM; sodium chloride 300 mM; DTT 5 mM

sample_conditions_2: ionic strength: 320 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_2isotropicsample_conditions_2
3D HNCOsample_2isotropicsample_conditions_2
3D HNCAsample_2isotropicsample_conditions_2
3D HN(CO)CACBsample_2isotropicsample_conditions_2
3D HN(CA)COsample_2isotropicsample_conditions_2
3D HN(CO)CAsample_2isotropicsample_conditions_2
3D HNNsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2
3D HMCM(CG)CBsample_2isotropicsample_conditions_2
3D HMCM(CGCB)CAsample_2isotropicsample_conditions_2
3D HNCACBsample_2isotropicsample_conditions_2

Software:

TOPSPIN - collection

NMRPipe - processing

NMRFAM-SPARKY - chemical shift assignment

NMR spectrometers:

  • Bruker AVANCE III 600 MHz

Related Database Links:

UNP O00571

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