BMRB Entry 31150

Name: Chemical shifts of CD28 hinge (I114-P152) used in chimeric antigen receptor (CAR) T-cells
Published: 2024-09-03

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PDB ID: 8w2v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31150
MolProbity Validation Chart

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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:

Chemical shifts of CD28 hinge (I114-P152) used in chimeric antigen receptor (CAR) T-cells

Deposition date:

2024-02-21

Original release date:

2024-09-03

Authors:

Folimonova, V.; Chen, X.; Schwieters, C.; Walters, K.

Citation:

Citation: Folimonova, Varvara; Chen, Xiang; Negi, Hitendra; Schwieters, Charles; Li, Jess; Byrd, R Andrew; Taylor, Naomi; Youkharibache, Philippe; Walters, Kylie. "CD28 hinge used in chimeric antigen receptor (CAR) T-cells exhibits local structure and conformational exchange amidst global disorder" Commun. Biol. 7, 1072-1072 (2024).
PubMed: 39217198

Assembly members:

Assembly members:
entity_1, polymer, 44 residues, 4719.481 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPLGSIEVMYPPPYLDNEKS NGTIIHVKGKHLCPSPLFPG PSKP

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	179
15N chemical shifts	33
1H chemical shifts	280

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 44 residues - 4719.481 Da.

1

GLY

PRO

LEU

GLY

SER

ILE

GLU

VAL

MET

TYR

2

PRO

TYR

LEU

ASP

ASN

GLU

LYS

SER

3

ASN

GLY

THR

ILE

HIS

VAL

LYS

GLY

LYS

4

HIS

LEU

CYS

PRO

SER

PRO

LEU

PHE

PRO

GLY

5

PRO

SER

LYS

PRO

Samples:

sample_1: CD28 hinge, [U-100% 13C; U-100% 15N], 0.5 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 2 mM; zinc sulphate 20 uM; pefabloc 1 mM; sodium azide 0.1%

sample_2: CD28 hinge, [U-100% 13C; U-100% 15N], 0.6 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 2 mM; zinc sulphate 20 uM; pefabloc 1 mM; sodium azide 0.1%

sample_3: CD28 hinge, [U-100% 13C; U-100% 15N], 0.45 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 2 mM; zinc sulphate 20 uM; pefabloc 1 mM; sodium azide 0.1%

sample_4: CD28 hinge, [U-100% 15N], 0.4 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 2 mM; zinc sulphate 20 uM; pefabloc 1 mM; sodium azide 0.1%

sample_5: CD28 hinge, [U-100% 15N], 0.28 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 2 mM; zinc sulphate 20 uM; pefabloc 1 mM; sodium azide 0.1%

sample_conditions_1: ionic strength: 70 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 70 mM; pH: 6.5; pressure: 1 atm; temperature: 284 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D CON	sample_1	isotropic	sample_conditions_1
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 HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D 1H-13C CCH TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HNCAN	sample_1	isotropic	sample_conditions_1
3D 1H-13C HCCH TOCSY	sample_2	isotropic	sample_conditions_1
2D CACO	sample_3	isotropic	sample_conditions_1
3D CANCO	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1
3D HNHB	sample_5	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_2
3D HNCO	sample_1	isotropic	sample_conditions_2
3D HN(CA)CO	sample_1	isotropic	sample_conditions_2
3D HNCO-COSY	sample_1	isotropic	sample_conditions_2

Software:

TopSpin, Bruker Biospin - collection

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

XEASY, Bartels et al. - data analysis, peak picking

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

TALOS+, Shen, Delaglio, Cornilescu and Bax - data analysis

MddNMR, Orekhov, Jaravine, Mayzel, Kazimierczuk - processing

NMR spectrometers:

Bruker AVANCE III 700 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 900 MHz
Bruker AVANCE III 850 MHz

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