BMRB Entry 30293
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30293
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 340 |
| 15N chemical shifts | 70 |
| 1H chemical shifts | 525 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 75 residues - 8521.567 Da.
| 1 | GLY | GLU | PHE | GLY | SER | MET | VAL | LYS | GLU | THR | ||||
| 2 | LYS | PHE | TYR | ASP | ILE | LEU | GLY | VAL | PRO | VAL | ||||
| 3 | THR | ALA | THR | ASP | VAL | GLU | ILE | LYS | LYS | ALA | ||||
| 4 | TYR | ARG | LYS | CYS | ALA | LEU | LYS | TYR | HIS | PRO | ||||
| 5 | ASP | LYS | ASN | PRO | SER | GLU | GLU | ALA | ALA | GLU | ||||
| 6 | LYS | PHE | LYS | GLU | ALA | SER | ALA | ALA | TYR | GLU | ||||
| 7 | ILE | LEU | SER | ASP | PRO | GLU | LYS | ARG | ASP | ILE | ||||
| 8 | TYR | ASP | GLN | PHE | GLY |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_4 | anisotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_4 | isotropic | sample_conditions_2 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_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