BMRB Entry 17858

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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/BMR17858
MolProbity Validation Chart

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Title:
RNA-binding zinc finger protein
Deposition date:
2011-08-12
Original release date:
2012-06-05
Authors:
Brockmann, Christoph; Neuhaus, David; Stewart, Murray
Citation:

Citation: Brockmann, Christoph; Soucek, Sharon; Kuhlmann, Sonja; Mills-Lujan, Katherine; Kelly, Seth; Yang, Ji-Chun; Iglesias, Nahid; Stutz, Francoise; Corbett, Anita; Neuhaus, David; Stewart, Murray. "Structural Basis for Polyadenosine-RNA Binding by Nab2 Zn Fingers and Its Function in mRNA Nuclear Export."  Structure 20, 1007-1018 (2012).
PubMed: 22560733

Assembly members:

Assembly members:
NAB2_404-483, polymer, 80 residues, 9227.831 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX6P-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
NAB2_404-483: GPLGSEKSLEQCKFGTHCTN KRCKYRHARSHIMCREGANC TRIDCLFGHPINEDCRFGVN CKNIYCLFRHPPGRVLPEKK

Data sets:
Data typeCount
13C chemical shifts268
15N chemical shifts80
1H chemical shifts530

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1NAB2_404-4831
2Zinc ions 12
3Zinc ions 22
4Zinc ions 32

Entities:

Entity 1, NAB2_404-483 80 residues - 9227.831 Da.

1   GLYPROLEUGLYSERGLULYSSERLEUGLU
2   GLNCYSLYSPHEGLYTHRHISCYSTHRASN
3   LYSARGCYSLYSTYRARGHISALAARGSER
4   HISILEMETCYSARGGLUGLYALAASNCYS
5   THRARGILEASPCYSLEUPHEGLYHISPRO
6   ILEASNGLUASPCYSARGPHEGLYVALASN
7   CYSLYSASNILETYRCYSLEUPHEARGHIS
8   PROPROGLYARGVALLEUPROGLULYSLYS

Entity 2, Zinc ions 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: TRIS, [U-2H], 50 mM; arginine 50 mM; glutamic acid 50 mM; zinc chloride 10 uM; mercaptoethanol, [U-2H], 5 mM; sodium chloride 50 mM; H2O 95%; D20 5%; NAB2_404-483, 15N,13C U, 1.2 mH

sample_2: TRIS, [U-2H], 50 mM; arginine 50 mM; glutamic acid 50 mM; zinc chloride 10 uM; mercaptoethanol, [U-2H], 5 mM; sodium chloride 50 mM; tobacco mosaic virus 25 mg/ml; H2O 95%; D20 5%; NAB2_404-483, 15N,13C U, 1.2 mH

sample_conditions_1: ionic strength: 0.125 M; pH: 6.75; pressure: 1 atm; temperature: 290 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQC lomg-range optimisedsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H[C]CH-TOCSYsample_1isotropicsample_conditions_1
3D [H]CCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESY (50ms mixing)sample_1isotropicsample_conditions_1
3D 1H-15N NOESY (120 ms mixing)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic (150 ms mixing)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromatic (150 ms mixing)sample_1isotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_2isotropicsample_conditions_1
3D HNCO IPAPsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - processing

Analysis, CCPN - chemical shift assignment, data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

  • Bruker DMX 600 MHz
  • Bruker DRX 500 MHz

Related Database Links:

PDB

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