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
MolProbity Validation Chart

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Title:
Solution structure of the S. cerevisiae H/ACA RNP protein Nhp2p-S82W mutant
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:

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).
PubMed: 21708174

Assembly members:

Assembly members:
Nhp2p-S82W, polymer, 121 residues, 13306.792 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: Saccharomyces cerevisiae   Vector: pET24a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Nhp2p-S82W: SKKLNKKVLKTVKKASKAKN VKRGVKEVVKALRKGEKGLV VIAGDIWPADVISHIPVLCE DHSVPYIFIPSKQDLGAAGA TKRPTSVVFIVPGSNKKKDG KNKEEEYKESFNEVVKEVQA L

Data sets:
Data typeCount
13C chemical shifts351
15N chemical shifts114
1H chemical shifts643

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1H/ACA RNP protein Nhp2p-S82W mutant1

Entities:

Entity 1, H/ACA RNP protein Nhp2p-S82W mutant 121 residues - 13306.792 Da.

1   SERLYSLYSLEUASNLYSLYSVALLEULYS
2   THRVALLYSLYSALASERLYSALALYSASN
3   VALLYSARGGLYVALLYSGLUVALVALLYS
4   ALALEUARGLYSGLYGLULYSGLYLEUVAL
5   VALILEALAGLYASPILETRPPROALAASP
6   VALILESERHISILEPROVALLEUCYSGLU
7   ASPHISSERVALPROTYRILEPHEILEPRO
8   SERLYSGLNASPLEUGLYALAALAGLYALA
9   THRLYSARGPROTHRSERVALVALPHEILE
10   VALPROGLYSERASNLYSLYSLYSASPGLY
11   LYSASNLYSGLUGLUGLUTYRLYSGLUSER
12   PHEASNGLUVALVALLYSGLUVALGLNALA
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:

NameSampleSample stateSample conditions
3D HNCACB13C_15N_sampleisotropicsample_conditions_1
3D CBCA(CO)NH13C_15N_sampleisotropicsample_conditions_1
3D HNCO13C_15N_sampleisotropicsample_conditions_1
3D HBHA(CO)NH15N_sampleisotropicsample_conditions_1
3D HCCH-TOCSY13C_15N_sampleisotropicsample_conditions_1
3D 1H-13C NOESY13C_15N_sample_2isotropicsample_conditions_1
3D 1H-15N NOESY15N_sampleisotropicsample_conditions_1
2D 1H-15N HSQC15N_sampleisotropicsample_conditions_1
2D 1H-13C HSQC13C_15N_sampleisotropicsample_conditions_1
3D C(CO)NH13C_15N_sampleisotropicsample_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
AlphaFold P32495

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