BMRB Entry 15644

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15644
MolProbity Validation Chart

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Title:
1H, 15N and 13C chemical shift assignments for Rds3 protein
Deposition date:
2008-01-31
Original release date:
2008-07-28
Authors:
Loening, Nikolaus; van Roon, Anne-Marie; Yang, Ji-Chun; Nagai, Kiyoshi; Neuhaus, David
Citation:

Citation: van Roon, Anne-Marie; Loening, Nikolaus; Obayashi, Eiji; Yang, Ji-Chun; Newman, Andrew; Hernandez, Helena; Nagai, Kiyoshi; Neuhaus, David. "Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif"  Proc. Natl. Acad. Sci. U. S. A. 105, 9621-9626 (2008).
PubMed: 18621724

Assembly members:

Assembly members:
Rds3p, polymer, 109 residues, 12353.605 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: pRK172

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Rds3p: GGSSRHQFDLIMCLKQPGVQ TGLLCEKCDGKCPICDSYVR PKRKVRVCENCSFGKQAKNC IICNLNVGVNDAFYCWECCR LGKDKDGCPRILNLGSNRLD RHFEKKKKV

Data sets:
Data typeCount
13C chemical shifts479
15N chemical shifts109
1H chemical shifts756

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Rds31
2ZINC ION_12
3ZINC ION_22
4ZINC ION_32

Entities:

Entity 1, Rds3 109 residues - 12353.605 Da.

residues -1 to 1 (GGS) result from cleavage of an N-terminal GST fusion protein

1   GLYGLYSERSERARGHISGLNPHEASPLEU
2   ILEMETCYSLEULYSGLNPROGLYVALGLN
3   THRGLYLEULEUCYSGLULYSCYSASPGLY
4   LYSCYSPROILECYSASPSERTYRVALARG
5   PROLYSARGLYSVALARGVALCYSGLUASN
6   CYSSERPHEGLYLYSGLNALALYSASNCYS
7   ILEILECYSASNLEUASNVALGLYVALASN
8   ASPALAPHETYRCYSTRPGLUCYSCYSARG
9   LEUGLYLYSASPLYSASPGLYCYSPROARG
10   ILELEUASNLEUGLYSERASNARGLEUASP
11   ARGHISPHEGLULYSLYSLYSLYSVAL

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Rds3p, [U-98% 15N], 350 uM; Tris buffer, [U-99% 2H], 20 mM; sodium chloride 200 mM; DTT, [U-99% 2H], 1 mM

sample_2: Rds3p, [U-98% 13C; U-98% 15N], 700 uM; Tris buffer, [U-99% 2H], 20 mM; sodium chloride 200 mM; DTT, [U-99% 2H], 1 mM

sample_conditions_1: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 15N T1sample_1isotropicsample_conditions_1
2D 15N T2sample_1isotropicsample_conditions_1
2D 15N NOEsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC full widthsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESY filtered (15N coupled 1H removed from F2)sample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNHAHBsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D H[C]CH-TOCSYsample_2isotropicsample_conditions_1
3D [H]CCH-TOCSYsample_2isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HACAHB-COSYsample_2isotropicsample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - processing

CCPN_analysis v1.0.15, CCPN - data analysis

ARIA v1.1.2, Linge, O'Donoghue and Nilges - refinement

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker DMX 600 MHz
  • Bruker DRX 500 MHz

Related Database Links:

PDB
DBJ GAA27055
EMBL CAY87048
GB AAB68140 AAT93199 AHY78252 AJP42220 AJV91308
REF NP_015419
SP Q06835
TPG DAA11509
AlphaFold Q06835

Download HSQC peak lists in one of the following formats:
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