BMRB Entry 52286

Name: Backbone Assignments of Ydj1 J-domain and Gly-rich region
Published: 2024-04-12

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52286

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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:

Backbone Assignments of Ydj1 J-domain and Gly-rich region

Deposition date:

2024-01-25

Original release date:

2024-04-12

Authors:

Ciesielski, Szymon; Tonelli, Marco; Craig, Elizabeth

Citation:

Citation: Ciesielski, Szymon; Schilke, Brenda; Stolarska, Milena; Tonelli, Marco; Tomiczek, Bartlomiej; Craig, Elizabeth. "Comparative structural and functional analysis of the glycine-rich regions of Class A and B J-domain protein cochaperones of Hsp70" FEBS Lett. 598, 1465-1477 (2024).
PubMed: 38529663

Assembly members:

Assembly members:
entity_1, polymer, 114 residues, Formula weight is not available

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: Escherichia coli Vector: pSmt3-ydj1109

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GEFGSMVKETKFYDILGVPV TATDVEIKKAYRKCALKYHP DKNPSEEAAEKFKEASAAYE ILSDPEKRDIYDQFGEDGLS GAGGAGGFPGGGFGFGDDIF SQFFGAGGAQRPRG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	205
15N chemical shifts	105
1H chemical shifts	105

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ydj1 J-domain and Gly-rich region (1-109 residues)	1

Entities:

Entity 1, Ydj1 J-domain and Gly-rich region (1-109 residues) 114 residues - Formula weight is not available

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

GLU

ASP

GLY

LEU

SER

9

GLY

ALA

GLY

ALA

GLY

PHE

PRO

GLY

10

GLY

PHE

GLY

PHE

GLY

ASP

ILE

PHE

11

SER

GLN

PHE

GLY

ALA

GLY

ALA

GLN

12

ARG

PRO

ARG

GLY

Samples:

sample_1: Ydj1 1-109, [U-100% 13C; U-100% 15N], 300 uM; TRIS 20 mM; sodium chloride 150 mM; DTT 5 mM; sodium azide 0.02%

sample_conditions_1: ionic strength: 300 mM; pH: 7.5; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN - collection

VNMRj - collection

NMRPipe - processing

SMILE - processing

NMRFAM-SPARKY - data analysis

PINE - data analysis

APES - data analysis

NMR spectrometers:

Bruker AVANCE III 900 MHz
Varian VXRS 800 MHz
Bruker AVANCE III 750 MHz
Bruker AVANCE III 600 MHz
Varian VXRS 600 MHz

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