BMRB Entry 17578
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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/BMR17578
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Title: Solution structure of the S. cerevisiae H/ACA RNP protein Nhp2p-S82W mutant PubMed: 21708174
Deposition date: 2011-04-07 Original release date: 2011-06-30
Authors: Koo, Bon-Kyung; Park, Chin-Ju; Fernandez, Cesar; Chim, Nicholas; Ding, Yi; Chanfreau, Guillaume; Feigon, Juli
Citation: Koo, Bon-Kyung; Park, Chin-Ju; Fernandez, Cesar; Chim, Nicholas; Ding, Yi; Chanfreau, Guillaume; Feigon, Juli. "Structure of H/ACA RNP protein Nhp2p reveals cis/trans isomerization of a conserved proline at the RNA and Nop10 binding interface." J. Mol. Biol. 411, 927-942 (2011).
Assembly members:
Nhp2p-S82W, polymer, 121 residues, 13306.792 Da.
Natural source: Common Name: baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi
Experimental source: Production method: recombinant technology Host organism: Saccharomyces cerevisiae
Entity Sequences (FASTA):
Nhp2p-S82W: SKKLNKKVLKTVKKASKAKN
VKRGVKEVVKALRKGEKGLV
VIAGDIWPADVISHIPVLCE
DHSVPYIFIPSKQDLGAAGA
TKRPTSVVFIVPGSNKKKDG
KNKEEEYKESFNEVVKEVQA
L
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 351 |
| 15N chemical shifts | 114 |
| 1H chemical shifts | 643 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | H/ACA RNP protein Nhp2p-S82W mutant | 1 |
Entities:
Entity 1, H/ACA RNP protein Nhp2p-S82W mutant 121 residues - 13306.792 Da.
| 1 | SER | LYS | LYS | LEU | ASN | LYS | LYS | VAL | LEU | LYS | ||||
| 2 | THR | VAL | LYS | LYS | ALA | SER | LYS | ALA | LYS | ASN | ||||
| 3 | VAL | LYS | ARG | GLY | VAL | LYS | GLU | VAL | VAL | LYS | ||||
| 4 | ALA | LEU | ARG | LYS | GLY | GLU | LYS | GLY | LEU | VAL | ||||
| 5 | VAL | ILE | ALA | GLY | ASP | ILE | TRP | PRO | ALA | ASP | ||||
| 6 | VAL | ILE | SER | HIS | ILE | PRO | VAL | LEU | CYS | GLU | ||||
| 7 | ASP | HIS | SER | VAL | PRO | TYR | ILE | PHE | ILE | PRO | ||||
| 8 | SER | LYS | GLN | ASP | LEU | GLY | ALA | ALA | GLY | ALA | ||||
| 9 | THR | LYS | ARG | PRO | THR | SER | VAL | VAL | PHE | ILE | ||||
| 10 | VAL | PRO | GLY | SER | ASN | LYS | LYS | LYS | ASP | GLY | ||||
| 11 | LYS | ASN | LYS | GLU | GLU | GLU | TYR | LYS | GLU | SER | ||||
| 12 | PHE | ASN | GLU | VAL | VAL | LYS | GLU | VAL | GLN | ALA | ||||
| 13 | LEU |
Samples:
13C_15N_sample: HEPES, [U-13C; U-15N], 20 mM; potassium chloride 200 mM; DTT 1 mM; H2O 90%; D2O 10%
15N_sample: HEPES, [U-15N], 20 mM; potassium chloride 200 mM; DTT 1 mM; H2O 90%; D2O 10%
13C_15N_sample_2: HEPES, [U-13C; U-15N], 20 mM; potassium chloride 200 mM; DTT 1 mM; D2O 10%
sample_conditions_1: ionic strength: 0.2 M; pH: 7.4; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCACB | 13C_15N_sample | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | 13C_15N_sample | isotropic | sample_conditions_1 |
| 3D HNCO | 13C_15N_sample | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | 15N_sample | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | 13C_15N_sample | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | 13C_15N_sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | 15N_sample | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | 15N_sample | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | 13C_15N_sample | isotropic | sample_conditions_1 |
| 3D C(CO)NH | 13C_15N_sample | isotropic | sample_conditions_1 |
Software:
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
SPARKY, Goddard - chemical shift assignment, data analysis, peak picking
TOPSPIN, Bruker Biospin - collection
ProcheckNMR, Laskowski and MacArthur - data analysis
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
xwinnmr, Bruker Biospin - collection
NMR spectrometers:
- Bruker DRX 800 MHz
- Bruker DRX 600 MHz
Related Database Links:
| BMRB | 17579 |
| PDB | |
| DBJ | GAA22045 |
| EMBL | CAA40885 CAA67483 CAA98786 CAY79077 |
| GB | AHY74809 AJP37550 AJU57662 AJU58365 AJU59054 |
| REF | NP_010073 |
| SP | P32495 |
| TPG | DAA11656 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts