BMRB Entry 34531

Name: Solution structure of the water-soluble LU-domain of human Lypd6b protein
Published: 2021-01-06

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PDB ID: 6zso
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34531
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:

Solution structure of the water-soluble LU-domain of human Lypd6b protein

Deposition date:

2020-07-16

Original release date:

2021-01-06

Authors:

Tsarev, A.; Kulbatskii, D.; Paramonov, A.; Lyukmanova, E.; Shenkarev, Z.

Citation:

Citation: Paramonov, Alexander; Kocharovskaya, Milita; Tsarev, Andrey; Kulbatskii, Dmitrii; Loktyushov, Eugene; Shulepko, Mikhail; Kirpichnikov, Mikhail; Lyukmanova, Ekaterina; Shenkarev, Zakhar. "Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors" Int. J. Mol. Sci. 21, 7280-7280 (2020).
PubMed: 33019770

Assembly members:

Assembly members:
entity_1, polymer, 96 residues, 11012.296 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) Vector: pET22b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MFKCFTCENAGDNYNCNRWA EDKWCPQNTQYCLTVHHFTS HGRSTSITKKCASRSECHFV GCHHSRDSEHTECRSCCEGM ICNVELPTNHTNAVFA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	373
15N chemical shifts	107
1H chemical shifts	596

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 96 residues - 11012.296 Da.

1

MET

PHE

LYS

CYS

PHE

THR

CYS

GLU

ASN

ALA

2

GLY

ASP

ASN

TYR

ASN

CYS

ASN

ARG

TRP

ALA

3

GLU

ASP

LYS

TRP

CYS

PRO

GLN

ASN

THR

GLN

4

TYR

CYS

LEU

THR

VAL

HIS

PHE

THR

SER

5

HIS

GLY

ARG

SER

THR

SER

ILE

THR

LYS

6

CYS

ALA

SER

ARG

SER

GLU

CYS

HIS

PHE

VAL

7

GLY

CYS

HIS

SER

ARG

ASP

SER

GLU

HIS

8

THR

GLU

CYS

ARG

SER

CYS

GLU

GLY

MET

9

ILE

CYS

ASN

VAL

GLU

LEU

PRO

THR

ASN

HIS

10

THR

ASN

ALA

VAL

PHE

ALA

Samples:

sample_1: lypd6, [U-13C; U-15N], 0.2 ± 0.02 mM

sample_conditions_1: ionic strength: 10 mM; pH: 5.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2d 1h-13C TROSY aromatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v3, Bruker Biospin - collection

MddNMR, V. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, Swedish NMR Center, University of Gothenburg - processing

CYANA v3.98.5, Guntert, Mumenthaler and Wuthrich - structure calculation

CARA v1.8, Keller and Wuthrich - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III 600 MHz

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