BMRB Entry 30293

Name: NMR structure of Ydj1 J-domain, a cytosolic Hsp40 from Saccharomyces cerevisiae
Published: 2017-10-23

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PDB ID: 5vso
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30293
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of Ydj1 J-domain, a cytosolic Hsp40 from Saccharomyces cerevisiae

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:

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).
PubMed: 29084221

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	340
15N chemical shifts	70
1H chemical shifts	525

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

ALA

4

TYR

ARG

LYS

CYS

ALA

LEU

LYS

TYR

HIS

PRO

5

ASP

LYS

ASN

PRO

SER

GLU

ALA

GLU

6

LYS

PHE

LYS

GLU

ALA

SER

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