BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 30293

Title: NMR structure of Ydj1 J-domain, a cytosolic Hsp40 from Saccharomyces cerevisiae   PubMed: 29084221

Deposition date: 2017-05-12 Original release date: 2017-10-23

Authors: Ciesielski, S.; Tonelli, M.; Lee, W.; Cornilescu, G.; Markley, J.; Schilke, B.; Ziegelhoffer, T.; Craig, E.

Citation: Schilke, Brenda; Ciesielski, Szymon; Ziegelhoffer, Thomas; Kamiya, Erina; Tonelli, Marco; Lee, Woonghee; Cornilescu, Gabriel; Hines, Justin; Markley, John; Craig, Elizabeth. "Broadening the functionality of a J-protein/Hsp70 molecular chaperone system."  PLoS Genet. 13, e1007084-e1007084 (2017).

Assembly members:
entity_1, polymer, 75 residues, 8521.567 Da.

Natural source:   Common Name: Baker's yeast   Taxonomy ID: 559292   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: GEFGSMVKETKFYDILGVPV TATDVEIKKAYRKCALKYHP DKNPSEEAAEKFKEASAAYE ILSDPEKRDIYDQFG

Data sets:
Data typeCount
13C chemical shifts340
15N chemical shifts70
1H chemical shifts525

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 75 residues - 8521.567 Da.

1   GLYGLUPHEGLYSERMETVALLYSGLUTHR
2   LYSPHETYRASPILELEUGLYVALPROVAL
3   THRALATHRASPVALGLUILELYSLYSALA
4   TYRARGLYSCYSALALEULYSTYRHISPRO
5   ASPLYSASNPROSERGLUGLUALAALAGLU
6   LYSPHELYSGLUALASERALAALATYRGLU
7   ILELEUSERASPPROGLULYSARGASPILE
8   TYRASPGLNPHEGLY

Samples:

sample_4: Ydj1 protein (1-70 residues), [U-15N], 5.5 ± 0.1 mg/mL; NaCl 150 mM

sample_1: Ydj1 protein (1-70 residues), [U-15N; U-13C], 3.5 ± 0.1 mg/mL; NaCl 150 mM

sample_2: Ydj1 protein (1-70 residues), [U-15N; U-13C], 4.0 ± 0.1 mg/mL; NaCl 150 mM

sample_3: Ydj1 protein (1-70 residues), [U-15N], 5.5 ± 0.1 mg/mL; NaCl 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.5; pressure: 1 atm; temperature: 279 K

sample_conditions_2: ionic strength: 150 mM; pH: 7.5; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_2
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_4anisotropicsample_conditions_2
2D 1H-15N HSQCsample_4isotropicsample_conditions_2
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1

Software:

APES, Shin, Lee and Lee - peak picking

AUDANA, Lee, Petit, Cornilescu, Stark and Markley - structure calculation

NMRFAM-SPARKY v1.41, Lee, Tonelli and Markley - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

PINE-SPARKY, Lee, Westler, Bahrami, Eghbalnia and Markley - chemical shift assignment

PONDEROSA-C/S, Lee, Stark and Markley - refinement, structure calculation

TOPSPIN, Bruker Biospin - collection

VNMR, Varian - collection

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

  • Bruker AvanceIII 900 MHz
  • Varian VXRS 800 MHz
  • Varian VXRS 600 MHz
  • Bruker AvanceIII 600 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts