BMRB Entry 34673

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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/BMR34673
MolProbity Validation Chart

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Title:
Solution structure of RBM39 RRM2 bound to 5'-AGCUUUG-3
Deposition date:
2021-10-26
Original release date:
2023-01-31
Authors:
Campagne, S.; Allain, F.
Citation:

Citation: Campagne, Sebastien; Jutzi, Daniel; Malard, Florian; Matoga, Maja; Romane, Ksenija; Feldmuller, Miki; Colombo, Martino; Ruepp, Marc-David; Allain, Frederic H-T. "Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39"  Nat. Commun. 14, 5366-5366 (2023).
PubMed: 37666821

Assembly members:

Assembly members:
entity_1, polymer, 93 residues, 10441.014 Da.
entity_2, polymer, 7 residues, 2198.339 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-Gold(DE3)pLysS AG'

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MAGPMRLYVGSLHFNITEDM LRGIFEPFGRIESIQLMMDS ETGRSKGYGFITFSDSECAK KALEQLNGFELAGRPMKVGH VTERTDALELVPR
entity_2: AGCUUUG

Data sets:
Data typeCount
13C chemical shifts360
15N chemical shifts87
1H chemical shifts638

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 93 residues - 10441.014 Da.

1   METALAGLYPROMETARGLEUTYRVALGLY
2   SERLEUHISPHEASNILETHRGLUASPMET
3   LEUARGGLYILEPHEGLUPROPHEGLYARG
4   ILEGLUSERILEGLNLEUMETMETASPSER
5   GLUTHRGLYARGSERLYSGLYTYRGLYPHE
6   ILETHRPHESERASPSERGLUCYSALALYS
7   LYSALALEUGLUGLNLEUASNGLYPHEGLU
8   LEUALAGLYARGPROMETLYSVALGLYHIS
9   VALTHRGLUARGTHRASPALALEUGLULEU
10   VALPROARG

Entity 2, unit_2 7 residues - 2198.339 Da.

1   AGCUUUG

Samples:

sample_1: NaPO4 10 mM; sodium chloride 50 mM; DTT 2 mM; RBM39 RRM2, [U-13C; U-15N], 1.2 mM; AGCUUUG 1.2 mM

sample_2: NaPO4 10 mM; sodium chloride 50 mM; DTT 2 mM; RBM39 RRM2, [U-13C; U-15N], 1.2 mM; AGCUUUG 1.2 mM

sample_conditions_1: ionic strength: 60 mM; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D F1FF2F NOESYsample_2isotropicsample_conditions_1
2D F2F NOESYsample_2isotropicsample_conditions_1
2D F2f TOCSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

ATNOS, Thorsten - peak picking

NMR spectrometers:

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

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