BMRB Entry 36452

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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/BMR36452
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
Solution structure of Rbfox RRM bound to a non-cognate RNA
Deposition date:
2021-10-23
Original release date:
2025-11-01
Authors:
Yang, F.; Varani, G.
Citation:

Citation: Ye, Xuan; Yang, Wen; Yi, Soon; Zhao, Yanan; Varani, Gabriele; Jankowsky, Eckhard; Yang, Fan. "Two distinct binding modes provide the RNA-binding protein RbFox with extraordinary sequence specificity."  Nat. Commun. 14, 701-701 (2023).
PubMed: 36759600

Assembly members:

Assembly members:
RNA (5'-R(*UP*GP*CP*AP*UP*AP*U)-3'), polymer, 7 residues, 2182.339 Da.
RNA binding protein fox-1 homolog 1, polymer, 102 residues, 11687.209 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 9606   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: chemical synthesis   Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA (5'-R(*UP*GP*CP*AP*UP*AP*U)-3'): UGCAUAU
RNA binding protein fox-1 homolog 1: HMNTENKSQPKRLHVSNIPF RFRDPDLRQMFGQFGKILDV EIIFNERGSKGFGFVTFENS ADADRAREKLHGTVVEGRKI EVNNATARVMTNKKTVNPYT NG

Data sets:
Data typeCount
13C chemical shifts415
15N chemical shifts111
1H chemical shifts657

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 7 residues - 2182.339 Da.

1   UGCAUAU

Entity 2, entity_2 102 residues - 11687.209 Da.

1   HISMETASNTHRGLUASNLYSSERGLNPRO
2   LYSARGLEUHISVALSERASNILEPROPHE
3   ARGPHEARGASPPROASPLEUARGGLNMET
4   PHEGLYGLNPHEGLYLYSILELEUASPVAL
5   GLUILEILEPHEASNGLUARGGLYSERLYS
6   GLYPHEGLYPHEVALTHRPHEGLUASNSER
7   ALAASPALAASPARGALAARGGLULYSLEU
8   HISGLYTHRVALVALGLUGLYARGLYSILE
9   GLUVALASNASNALATHRALAARGVALMET
10   THRASNLYSLYSTHRVALASNPROTYRTHR
11   ASNGLY

Samples:

sample_1: protein, [U-15N], 1 mM; RNA 1.2 mM; sodium azide 0.05 % w/v; sodium chloride 30 mM; sodium phosphate 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: protein, [U-13C; U-15N], 1 mM; RNA 1.2 mM; sodium azide 0.05 % w/v; sodium chloride 30 mM; sodium phosphate 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: protein, [U-15N; U-13C], 1 mM; RNA 1.2 mM; sodium azide 0.05 % w/v; sodium chloride 30 mM; sodium phosphate 10 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 40 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D NHCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D NH(CA)COsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
2D F1-F2- filtered NOESYsample_3isotropicsample_conditions_1
2D TOCSYsample_3isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

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

CcpNmr Analysis, CCPN - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Bruker AVANCE 800 MHz

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