BMRB Entry 34465

Title:
Structure of a protein-RNA complex by ssNMR   PubMed: 32023357
Deposition date:
2019-12-13
Original release date:
2020-02-06
Authors:
Mumdooh, A.; Marchanka, A.; Carlomagno, T.
Citation:

Citation: Ahmed, M.; Marchanka, A.; Carlomagno, T.. "Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy"  Angew. Chem. Int. Ed. Engl. 59, 6866-6873 (2020).

Assembly members:

Assembly members:
entity_1, polymer, 123 residues, 13414.664 Da.
entity_2, polymer, 26 residues, 8407.075 Da.

Natural source:

Natural source:   Common Name: Pyrococcus furiosus   Taxonomy ID: 2261   Superkingdom: Archaea   Kingdom: not available   Genus/species: Pyrococcus furiosus

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

Experimental source:

Natural source:   Common Name: Pyrococcus furiosus   Taxonomy ID: 2261   Superkingdom: Archaea   Kingdom: not available   Genus/species: Pyrococcus furiosus

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

Data sets:
Data typeCount
13C chemical shifts327
15N chemical shifts98

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 123 residues - 13414.664 Da.

1   METALALYSPROSERTYRVALLYSPHEGLU
2   VALPROLYSGLULEUALAGLULYSALALEU
3   GLNALAVALGLUILEALAARGASPTHRGLY
4   LYSILEARGLYSGLYTHRASNGLUTHRTHR
5   LYSALAVALGLUARGGLYGLNALALYSLEU
6   VALILEILEALAGLUASPVALASPPROGLU
7   GLUILEVALALAHISLEUPROPROLEUCYS
8   GLUGLULYSGLUILEPROTYRILETYRVAL
9   PROSERLYSLYSGLULEUGLYALAALAALA
10   GLYILEGLUVALALAALAALASERVALALA
11   ILEILEGLUPROGLYLYSALAARGASPLEU
12   VALGLUGLUILEALAMETLYSVALLYSGLU
13   LEUMETLYS

Entity 2, entity_2 26 residues - 8407.075 Da.

1   GCUGAGCUCG
2   AAAGAGCAAU
3   GAUGUC

Samples:

sample_1: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_2: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 8 mg/mL; RNA (26-MER) 5 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_3: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; RNA (26-MER) 10 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 12 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_4: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ade), [U-13C; U-15N]-Ade, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_5: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ura), [U-13C; U-15N]-Ura, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_6: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; RNA (26-MER) 10 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 12 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_7: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ade), [U-13C; U-15N]-Ade, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_8: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ura), [U-13C; U-15N]-Ura, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_9: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; RNA (26-MER) 10 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 12 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_10: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ade), [U-13C; U-15N]-Ade, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_11: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ura), [U-13C; U-15N]-Ura, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.6; pressure: 1 bar; temperature: 265 K

sample_conditions_2: ionic strength: 150 mM; pH: 7.6; pressure: 1 bar; temperature: 260 K

Experiments:

NameSampleSample stateSample conditions
2D NCAsample_1anisotropicsample_conditions_1
2D NCOsample_1anisotropicsample_conditions_1
2D 13C,13C DARRsample_1anisotropicsample_conditions_1
3D NCACXsample_2anisotropicsample_conditions_1
3D NCOCXsample_2anisotropicsample_conditions_1
2D 13C,13C DARRsample_2anisotropicsample_conditions_1
3D CANCOsample_2anisotropicsample_conditions_1
2D 13C,13C SPC53sample_2anisotropicsample_conditions_1
2D 13C,13C SPC53sample_3anisotropicsample_conditions_2
2D 13C,13C SPC53sample_4anisotropicsample_conditions_2
2D 13C,13C SPC53sample_6anisotropicsample_conditions_2
2D 13C,13C SPC53sample_5anisotropicsample_conditions_2
2D 13C,13C SPC53sample_7anisotropicsample_conditions_2
2D 13C,13C SPC53sample_8anisotropicsample_conditions_2
2D 13C,13C SPC53sample_9anisotropicsample_conditions_2
2D 13C,13C SPC53sample_10anisotropicsample_conditions_2
2D 13C,13C SPC53sample_11anisotropicsample_conditions_2

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

HADDOCK, Bonvin - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

TopSpin, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AVANCE III 600 MHz