BMRB Entry 50912

Name: Structure of the transmembrane domain of the CD28 dimer
Published: 2022-03-01

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50912

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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:

Structure of the transmembrane domain of the CD28 dimer

Deposition date:

2021-04-23

Original release date:

2022-03-01

Authors:

Wen, Maorong; Ouyang, Bo; Wu, Hongyi; Cao, Ruiyu; Wu, Bin

Citation:

Citation: Wu, Hongyi; Cao, Ruiyu; Wen, Maorong; Xue, Hongjuan; OuYang, Bo. "Structural characterization of a dimerization interface in the CD28 transmembrane domain" Structure 30, 803-812 (2022).
PubMed: 35397202

Assembly members:

Assembly members:
entity_1, polymer, 41 residues, Formula weight is not available

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 Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPSKPFWVLVVVGGVLAFYS LLVTVAFIIFWVRSKRSRLL H

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	151
15N chemical shifts	38
1H chemical shifts	262

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CD28 dimer, subunit 1	1
2	CD28 dimer, subunit 2	1

Entities:

Entity 1, CD28 dimer, subunit 1 41 residues - Formula weight is not available

1

GLY

PRO

SER

LYS

PRO

PHE

TRP

VAL

LEU

VAL

2

VAL

GLY

VAL

LEU

ALA

PHE

TYR

SER

3

LEU

VAL

THR

VAL

ALA

PHE

ILE

PHE

4

TRP

VAL

ARG

SER

LYS

ARG

SER

ARG

LEU

5

HIS

Samples:

sample_1: CD28 TM, [U-13C; U-15N; 75%-2H], 0.6 mM; MES 25 mM; DMPC 30 mM; DHPC 60 mM

sample_2: CD28 TM, [U-13C; U-15N], 0.6 mM; MES 25 mM; DMPC, [acyl chain U-2H], 30 mM; DHPC, [acyl chain U-2H], 60 mM

sample_3: CD28 TM, [U-15N; U-2H], 0.6 mM; MES 25 mM; DMPC, [acyl chain U-2H], 30 mM; DHPC, [acyl chain U-2H], 60 mM; CD28 TM, [U-13C], 0.6 mM

sample_4: CD28 TM, [U-15N; 15%-13C], 0.2 mM; MES 25 mM; DMPC, [acyl chain U-2H], 30 mM; DHPC, [acyl chain U-2H], 60 mM

sample_conditions_1: pH: 6.0; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
TROSY-HSQC	sample_1	isotropic	sample_conditions_1
TROSY-HNCO	sample_1	isotropic	sample_conditions_1
TROSY-HNCACO	sample_1	isotropic	sample_conditions_1
TROSY-HNCA	sample_1	isotropic	sample_conditions_1
TROSY-HNCOCA	sample_1	isotropic	sample_conditions_1
TROSY-HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.44 - refinement, structure calculation

NMRPipe - processing

XEASY - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 900 MHz

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