BMRB Entry 34108

Name: NMR structure of TLR4 transmembrane domain (624-670) in DMPG/DHPC bicelles
Published: 2017-08-31

Click here to enlarge.

PDB ID: 5nam
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34108
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

NMR structure of TLR4 transmembrane domain (624-670) in DMPG/DHPC bicelles

Deposition date:

2017-02-28

Original release date:

2017-08-31

Authors:

Mineev, K.; Goncharuk, S.; Goncharuk, M.; Arseniev, A.

Citation:

Citation: Mineev, K.; Goncharuk, S.; Goncharuk, M.; Volynsky, P.; Novikova, E.; Aresinev, A.. "Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism." Sci. Rep. 7, 6864-6864 (2017).
PubMed: 28761155

Assembly members:

Assembly members:
entity_1, polymer, 48 residues, 5282.465 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MNITSQMNKTIIGVSVLSVL VVSVVAVLVYKFYFHLMLLA GCIKYGRG

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	657
15N chemical shifts	145
1H chemical shifts	1098

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 48 residues - 5282.465 Da.

1

MET

ASN

ILE

THR

SER

GLN

MET

ASN

LYS

THR

2

ILE

GLY

VAL

SER

VAL

LEU

SER

VAL

LEU

3

VAL

SER

VAL

ALA

VAL

LEU

VAL

TYR

4

LYS

PHE

TYR

PHE

HIS

LEU

MET

LEU

ALA

5

GLY

CYS

ILE

LYS

TYR

GLY

ARG

GLY

Samples:

sample_1: DHPC 71 ± 1 mM; DMPG 29 ± 1 mM; TLR4-TM, [U-13C; U-15N], 0.5 ± 0.05 mM; imidazole 10 mM; sodium azide 0.01%

sample_2: DHPC 71 ± 1 mM; DMPC 29 ± 1 mM; TLR4-TM, [U-13C; U-15N], 0.5 ± 0.05 mM; imidazole 10 mM; sodium azide 0.01%

sample_3: DPC, [U-2H], 50 ± 1 mM; TLR4-TM, [U-13C; U-15N], 0.5 ± 0.05 mM; imidazole 10 mM; sodium azide 0.01%

sample_conditions_1: ionic strength: 10 mM; pH: 6.0; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_3	isotropic	sample_conditions_1
3D HNCA	sample_3	isotropic	sample_conditions_1

Software:

CARA v1.9.1, Keller and Wuthrich - chemical shift assignment

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

TOPSPIN v3.5, Bruker Biospin - processing

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 800 MHz

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