BMRB Entry 34766

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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/BMR34766
MolProbity Validation Chart

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Title:
NMR solution structure of the N-terminal RRM and flanking linker regions of Polypyrimidine tract binding protein 1 using the CYANA CONSENSUS method.
Deposition date:
2022-10-27
Original release date:
2023-10-31
Authors:
Damberger, F.; Beusch, I.; Allain, F.
Citation:

Citation: Damberger, F.; Krepl, M.; Beusch, I.; Dorn, G.; Maris, C.; Sponer, J.; Ravindranathan, S.; Allain, F.. "N-terminal domain of Polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition"  .

Assembly members:

Assembly members:
entity_1, polymer, 123 residues, 13375.167 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)   Vector: pTYB11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GNDSKKFKGDSRSAGVPSRV IHIRKLPIDVTEGEVISLGL PFGKVTNLLMLKGKNQAFIE MNTEEAANTMVNYYTSVTPV LRGQPIYIQFSNHKELKTDS SPNQARAQAALQAVNSVQSG NLA

Data sets:
Data typeCount
13C chemical shifts514
15N chemical shifts134
1H chemical shifts849

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 123 residues - 13375.167 Da.

1   GLYASNASPSERLYSLYSPHELYSGLYASP
2   SERARGSERALAGLYVALPROSERARGVAL
3   ILEHISILEARGLYSLEUPROILEASPVAL
4   THRGLUGLYGLUVALILESERLEUGLYLEU
5   PROPHEGLYLYSVALTHRASNLEULEUMET
6   LEULYSGLYLYSASNGLNALAPHEILEGLU
7   METASNTHRGLUGLUALAALAASNTHRMET
8   VALASNTYRTYRTHRSERVALTHRPROVAL
9   LEUARGGLYGLNPROILETYRILEGLNPHE
10   SERASNHISLYSGLULEULYSTHRASPSER
11   SERPROASNGLNALAARGALAGLNALAALA
12   LEUGLNALAVALASNSERVALGLNSERGLY
13   ASNLEUALA

Samples:

sample_1: Polypyrimidine-tract binding protein N-terminal RNA recognition motif, [U-15N]-99%, 0.8 ± 0.05 mM; NaH2PO4/NaOH buffer, none, 10 ± 0.5 mM; sodium chloride, none, 20 ± 0.5 mM

sample_2: Polypyrimidine-tract binding protein N-terminal RNA recognition motif, [U-13C; U-15N]-99%, 0.8 ± 0.05 mM; NaH2PO4/NaOH buffer, none, 10 ± 0.5 mM; sodium chloride, none, 20 ± 0.5 mM

sample_3: Polypyrimidine-tract binding protein N-terminal RNA recognition motif, [U-15N]-99%, 0.8 ± 0.05 mM; NaH2PO4/NaOH buffer, none, 10 ± 0.5 mM; sodium chloride, none, 20 ± 0.5 mM

sample_4: Polypyrimidine-tract binding protein N-terminal RNA recognition motif, [U-15N]-99%, 0.8 ± 0.05 mM; NaH2PO4/NaOH buffer, none, 10 ± 0.5 mM; sodium chloride, none, 20 ± 0.5 mM; UCUUU-SL-RNA, [U-13C,15N]-99%, 0.8 ± 0.05 mM

sample_conditions_1: ionic strength: 33.3 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 33.3 mM; pH: 6.5; pressure: 1 atm; temperature: 313 K

sample_conditions_3: ionic strength: 33.3 mM; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
15N T1-relaxation-15HSQCsample_1isotropicsample_conditions_2
15N T2-relaxation-T1rho-15NHSQCsample_1isotropicsample_conditions_2
{1H}15N-NOE-15NHSQCsample_1isotropicsample_conditions_2
relaxation-compensated IzNz Rex HSQCsample_1isotropicsample_conditions_1
15N T2-relaxation-dispersion CPMG-15NHSQCsample_1isotropicsample_conditions_1
15N T2-relaxation-dispersion-CPMG-15NHSQCsample_1isotropicsample_conditions_1
15N T2-relaxation-dispersion-CPMG-15NHSQCsample_3isotropicsample_conditions_3
cross-correlated DD/CSA relaxation-15NHSQCsample_1isotropicsample_conditions_1

Software:

CYANA v3.97beta, Guntert & Buchner, Wurz & Guntert - peak picking, refinement, structure calculation

TopSpin v3, Bruker Biospin - processing

CARA v1.9.1.7, Keller and Wuthrich - chemical shift assignment

NMR spectrometers:

  • Bruker AVANCE 900 MHz
  • Bruker AVANCE 750 MHz
  • Bruker AVANCE 700 MHz
  • Bruker AVANCE 500 MHz

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