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Biological Magnetic Resonance Data Bank


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BMRB Entry 25800

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25800
MolProbity Validation Chart

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Title: Solution structure of Plasmodium falciparum SR1-RRM1 in complex with ACAUCA RNA   PubMed: 30500338

Deposition date: 2015-09-08 Original release date: 2016-10-06

Authors: Ganguly, Akshay; Verma, Garima; Bhavesh, Neel Sarovar

Citation: Ganguly, Akshay; Verma, Garima; Bhavesh, Neel Sarovar. "The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition"  J. Mol. Biol. ., .-. (2018).

Assembly members:
PfSR1-RRM1, polymer, 89 residues, 9997.284 Da.
RNA_(5'-R(*AP*CP*AP*UP*CP*A)-3'), polymer, 6 residues, 1859.203 Da.

Natural source:   Common Name: malaria parasite P. falciparum   Taxonomy ID: 5833   Superkingdom: Eukaryota   Kingdom: not available   Genus/species: Plasmodium falciparum

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
PfSR1-RRM1: GSHMVIRESVSRIYVGNLPS HVSSRDVENEFRKYGNILKC DVKKTVSGAAFAFIEFEDAR DAADAIKEKDGCDFEGNKLR VEVPFNARE
RNA_(5'-R(*AP*CP*AP*UP*CP*A)-3'): ACAUCA

Data sets:
Data typeCount
13C chemical shifts398
15N chemical shifts84
1H chemical shifts374

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2RNA (5'-R(*AP*CP*AP*UP*CP*A)-3')2

Entities:

Entity 1, entity_1 89 residues - 9997.284 Da.

G-2, S-1, H0 are from pet28a vector

1   GLYSERHISMETVALILEARGGLUSERVAL
2   SERARGILETYRVALGLYASNLEUPROSER
3   HISVALSERSERARGASPVALGLUASNGLU
4   PHEARGLYSTYRGLYASNILELEULYSCYS
5   ASPVALLYSLYSTHRVALSERGLYALAALA
6   PHEALAPHEILEGLUPHEGLUASPALAARG
7   ASPALAALAASPALAILELYSGLULYSASP
8   GLYCYSASPPHEGLUGLYASNLYSLEUARG
9   VALGLUVALPROPHEASNALAARGGLU

Entity 2, RNA (5'-R(*AP*CP*AP*UP*CP*A)-3') 6 residues - 1859.203 Da.

1   ACAUCA

Samples:

sample_H2O: PfSR1-RRM1, [U-100% 13C; U-100% 15N], 0.5 – 1 mM; RNA (5'-R(*AP*CP*AP*UP*CP*A)-3')0.5 – 1 mM; sodium phosphate 25 mM; sodium chloride 100 mM; TCEP 3 mM; H2O 90%; D2O 10%

sample_D2O: PfSR1-RRM1, [U-100% 13C; U-100% 15N], 0.5 – 1 mM; RNA (5'-R(*AP*CP*AP*UP*CP*A)-3')0.5 – 1 mM; sodium phosphate 25 mM; sodium chloride 100 mM; TCEP 3 mM; D2O 100%

sample_conditions_1: ionic strength: 125 mM; pH: 5.9; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_H2Oisotropicsample_conditions_1
3D HNCACBsample_H2Oisotropicsample_conditions_1
2D 1H-1H NOESYsample_H2Oisotropicsample_conditions_1
2D 1H-1H TOCSYsample_H2Oisotropicsample_conditions_1
3D 1H-15N NOESYsample_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_D2Oisotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_D2Oisotropicsample_conditions_1
2D 1H-1H TOCSYsample_D2Oisotropicsample_conditions_1
2D 1H-1H NOESYsample_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_H2Oisotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_H2Oisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_D2Oisotropicsample_conditions_1
2D 13C(F1)-filtered, 13C(F2)-filtered 1H-1H NOESYsample_D2Oisotropicsample_conditions_1
2D 13C(F2)-edited 1H-1H NOESY aromaticsample_D2Oisotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA v1.8.4, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure solution

AMBER v15, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 700 MHz

Related Database Links:

NCBI XP_001351730.2

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts