BMRB Entry 34584

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34584
MolProbity Validation Chart

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Title:
Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA
Deposition date:
2020-12-17
Original release date:
2021-07-12
Authors:
Wurm, J.; Sprangers, R.
Citation:

Citation: Wurm, Jan Philip; Glowacz, Katarzyna-Anna; Sprangers, Remco. "Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome"  Proc. Natl. Acad. Sci. U. S. A. 118, e2105961118-e2105961118 (2021).
PubMed: 34453003

Assembly members:

Assembly members:
entity_1, polymer, 251 residues, 27014.055 Da.

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 83333   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGSTDALPPIEQQFYETSSK GKIPLLQRLLSLHQPSSCVV FCNTKKDCQAVCDALNEVGQ SALSLHGDLEQRDRDQTLVR FANGSARVLVATDVAARGLD IKSLELVVNFELAWDPEVHV HRIGRTARAGNSGLAISFCA PEEAQRANIISDMLQIKLNW QTPPANSSIATLEAEMATLC IDGGKKAKMRPGDVLGALTG DIGLDGADIGKIAVHPAHVY VAVRQAVAHKAWKQLQGGKI KGKTCRVRLLK

Data sets:
Data typeCount
13C chemical shifts804
15N chemical shifts251
1H chemical shifts738

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 251 residues - 27014.055 Da.

1   GLYGLYSERTHRASPALALEUPROPROILE
2   GLUGLNGLNPHETYRGLUTHRSERSERLYS
3   GLYLYSILEPROLEULEUGLNARGLEULEU
4   SERLEUHISGLNPROSERSERCYSVALVAL
5   PHECYSASNTHRLYSLYSASPCYSGLNALA
6   VALCYSASPALALEUASNGLUVALGLYGLN
7   SERALALEUSERLEUHISGLYASPLEUGLU
8   GLNARGASPARGASPGLNTHRLEUVALARG
9   PHEALAASNGLYSERALAARGVALLEUVAL
10   ALATHRASPVALALAALAARGGLYLEUASP
11   ILELYSSERLEUGLULEUVALVALASNPHE
12   GLULEUALATRPASPPROGLUVALHISVAL
13   HISARGILEGLYARGTHRALAARGALAGLY
14   ASNSERGLYLEUALAILESERPHECYSALA
15   PROGLUGLUALAGLNARGALAASNILEILE
16   SERASPMETLEUGLNILELYSLEUASNTRP
17   GLNTHRPROPROALAASNSERSERILEALA
18   THRLEUGLUALAGLUMETALATHRLEUCYS
19   ILEASPGLYGLYLYSLYSALALYSMETARG
20   PROGLYASPVALLEUGLYALALEUTHRGLY
21   ASPILEGLYLEUASPGLYALAASPILEGLY
22   LYSILEALAVALHISPROALAHISVALTYR
23   VALALAVALARGGLNALAVALALAHISLYS
24   ALATRPLYSGLNLEUGLNGLYGLYLYSILE
25   LYSGLYLYSTHRCYSARGVALARGLEULEU
26   LYS

Samples:

sample_1: DbpA residues 209-457, [U-2H; U-15N; NA-Y; methyl 13C,1H-ILMVAT], 0.8 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM

sample_2: DbpA residues 209-457, [U-2H; U-15N; NA-Y; methyl 13C,1H-ILMVAT], 0.8 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM

sample_3: DbpA residues 209-457, [U-10% 13C], 0.74 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM

sample_4: DbpA residues 209-457, [U-2H; U-15N; methyl 13C,1H-ILMVA], 0.8 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM

sample_5: DbpA residues 209-457, [U-13C; U-15N; U-2H; U-13C/U-2H/methyl-1H ILV], 0.74 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM

sample_conditions_1: ionic strength: 290 mM; pH: 7.3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNH NOESYsample_4isotropicsample_conditions_1
3D HNCACBsample_5isotropicsample_conditions_1
3D HNCOsample_5isotropicsample_conditions_1
3D HN(COCA)CBsample_5isotropicsample_conditions_1
3D HNCAsample_5isotropicsample_conditions_1
3D CNH NOESYsample_4isotropicsample_conditions_1
3D HCH NOESYsample_4isotropicsample_conditions_1
3D CCH NOESYsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_5isotropicsample_conditions_1
3D H(CCO)NHsample_5isotropicsample_conditions_1
3D HN(CA)COsample_5isotropicsample_conditions_1
3D HCH NOESYsample_2isotropicsample_conditions_1
3D HNH NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D CCH NOESYsample_4isotropicsample_conditions_1

Software:

CYANA v3.98.5, Guntert, Mumenthaler and Wuthrich - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

NMRFAM-SPARKY v1.414, W. Lee - peak picking

NMR spectrometers:

  • Bruker AVANCE NEO 800 MHz
  • Bruker AVANCE NEO 600 MHz

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