BMRB Entry 34675

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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/BMR34675
MolProbity Validation Chart

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Title:
The solution structure of hsDND1 RRM12 bound to CUUAUUUG RNA
Deposition date:
2021-10-31
Original release date:
2022-04-29
Authors:
Duszczyk, M.; Allain, F.
Citation:

Citation: Duszczyk, M.; Wischnewski, H.; Kazeeva, T.; Arora, R.; Loughlin, F.; von Schroetter, C.; Pradere, U.; Hall, J.; Ciaudo, C.; Allain, F.. "The solution structure of Dead End bound to AU-rich RNA reveals an unusual mode of tandem RRM-RNA recognition required for mRNA regulation"  Nat. Commun. 13, 5892-5892 (2022).
PubMed: 36202814

Assembly members:

Assembly members:
entity_1, polymer, 227 residues, 24927.939 Da.
entity_2, polymer, 8 residues, 2465.465 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMERVNPENKAALEAWVRE TGIRLVQVNGQRKYGGPPPG WVGSPPPAGSEVFIGRLPQD VYEHQLIPLFQRVGRLYEFR LMMTFSGLNRGFAYARYSSR RGAQAAIATLHNHPLRPSCP LLVCRSTEKCELSVDGLPPN LTRSALLLALQPLGPGLQEA RLLPSPGPAPGQIALLKFSS HRAAAMAKKALVEGQSHLCG EQVAVEWLKPDLKQRLRQQL VGPFLRS
entity_2: CUUAUUUG

Data sets:
Data typeCount
13C chemical shifts637
15N chemical shifts202
1H chemical shifts1461

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 227 residues - 24927.939 Da.

1   GLYALAMETGLUARGVALASNPROGLUASN
2   LYSALAALALEUGLUALATRPVALARGGLU
3   THRGLYILEARGLEUVALGLNVALASNGLY
4   GLNARGLYSTYRGLYGLYPROPROPROGLY
5   TRPVALGLYSERPROPROPROALAGLYSER
6   GLUVALPHEILEGLYARGLEUPROGLNASP
7   VALTYRGLUHISGLNLEUILEPROLEUPHE
8   GLNARGVALGLYARGLEUTYRGLUPHEARG
9   LEUMETMETTHRPHESERGLYLEUASNARG
10   GLYPHEALATYRALAARGTYRSERSERARG
11   ARGGLYALAGLNALAALAILEALATHRLEU
12   HISASNHISPROLEUARGPROSERCYSPRO
13   LEULEUVALCYSARGSERTHRGLULYSCYS
14   GLULEUSERVALASPGLYLEUPROPROASN
15   LEUTHRARGSERALALEULEULEUALALEU
16   GLNPROLEUGLYPROGLYLEUGLNGLUALA
17   ARGLEULEUPROSERPROGLYPROALAPRO
18   GLYGLNILEALALEULEULYSPHESERSER
19   HISARGALAALAALAMETALALYSLYSALA
20   LEUVALGLUGLYGLNSERHISLEUCYSGLY
21   GLUGLNVALALAVALGLUTRPLEULYSPRO
22   ASPLEULYSGLNARGLEUARGGLNGLNLEU
23   VALGLYPROPHELEUARGSER

Entity 2, unit_2 8 residues - 2465.465 Da.

1   CUUAUUUG

Samples:

sample_1: hsDnd1 RRM12, fractionally deuterated, 13C,15N-labeled, 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3') 0.9 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_2: hsDnd1 RRM12, [U-13C; U-15N], 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3') 0.9 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_3: hsDnd1 RRM12 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3') 0.8 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_4: hsDnd1 RRM12 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), selectively 13C ribose-labeled C*UU*AU*UU*G, 0.8 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_5: hsDnd1 RRM12, [U-13C; U-15N], 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3') 0.9 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_6: hsDnd1 RRM12 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), selectively 13C ribose-labeled CU*UA*UU*UG*, 0.8 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_7: hsDnd1 RRM12, 13C15N, 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), selectively 13C ribose-labeled C*UU*AU*UU*G, 0.8 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_8: hsDnd1 RRM12, [U-13C; U-15N], 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3'), selectively 13C ribose-labeled CU*UA*UU*UG*, 0.8 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_9: hsDnd1 RRM12, [U-13C; U-15N], 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3') 0.9 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM; C12E5 polyethylene glycol / hexanol 4.2%

sample_10: hsDnd1 RRM12, [U-13C; U-15N], 0.8 mM; RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3') 0.9 mM; KHPO4/ KH2PO4 pH 6.6 100 mM; DTT 1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.6; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D HNCO TROSYsample_1isotropicsample_conditions_1
3D HN(CA)CO TROSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_5isotropicsample_conditions_1
3D HN(CO)CACB TROSYsample_1isotropicsample_conditions_1
3D HNCACB TROSYsample_1isotropicsample_conditions_1
3D HN(CO)CA TROSYsample_1isotropicsample_conditions_1
3D HNCA TROSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D F1 filtered, F2 filtered NOESYsample_5isotropicsample_conditions_1
2D F2 filtered NOESYsample_5isotropicsample_conditions_1
2D NOESYsample_3isotropicsample_conditions_1
2D TOCSYsample_3isotropicsample_conditions_1
3D HCCH-COSYsample_5isotropicsample_conditions_1
3D HCCH-TOCSYsample_5isotropicsample_conditions_1
3D HCCH-TOCSYsample_5isotropicsample_conditions_1
3D 1H-13C-HSQC-aromatic-NOESYsample_5isotropicsample_conditions_1
3D 1H-13C-HMQC-NOESYsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_6isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D F2 filtered NOESYsample_8isotropicsample_conditions_1
2D F2 filtered NOESYsample_7isotropicsample_conditions_1
2D F1 filtered, F2 filtered NOESYsample_8isotropicsample_conditions_1
2D F1 filtered, F2 filtered NOESYsample_7isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
3D F3 filtered, F2 edited 13C HMQC-NOESYsample_5isotropicsample_conditions_1
2D 13C F2 filtered 2D NOESYsample_5isotropicsample_conditions_1
2D 13C F1 filtered, F2 filtered NOESYsample_5isotropicsample_conditions_1
2D 1H-15N TROSYsample_9anisotropicsample_conditions_1
2D 1H-15N TROSYsample_10isotropicsample_conditions_1

Software:

TopSpin v2.1, Bruker Biospin - collection

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

NMRFAM-SPARKY v1.1412, Lee W, Tonelli M, Markley JL - data analysis

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - structure calculation

Amber v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

ATNOS v3.1, ATNOS-CANDID - peak picking

Sparky, Goddard - chemical shift assignment

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

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE 900 MHz

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