BMRB Entry 34333

Name: Solution structure of the water-soluble LU-domain of human Lypd6 protein
Published: 2019-12-13

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PDB ID: 6ib6
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34333
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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 Lypd6 protein

Deposition date:

2018-11-29

Original release date:

2019-12-13

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:
Ly6/PLAUR domain-containing protein 6, polymer, 96 residues, 10941.329 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(+)/lypd6

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ly6/PLAUR domain-containing protein 6: MFKCFTCEKAADNYECNRWA PDIYCPRETRYCYTQHTMEV TGNSISVTKRCVPLEECLST GCRDSEHEGHKVCTSCCEGN ICNLPLPRNETDATFA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	354
15N chemical shifts	97
1H chemical shifts	603

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 96 residues - 10941.329 Da.

1

MET

PHE

LYS

CYS

PHE

THR

CYS

GLU

LYS

ALA

2

ALA

ASP

ASN

TYR

GLU

CYS

ASN

ARG

TRP

ALA

3

PRO

ASP

ILE

TYR

CYS

PRO

ARG

GLU

THR

ARG

4

TYR

CYS

TYR

THR

GLN

HIS

THR

MET

GLU

VAL

5

THR

GLY

ASN

SER

ILE

SER

VAL

THR

LYS

ARG

6

CYS

VAL

PRO

LEU

GLU

CYS

LEU

SER

THR

7

GLY

CYS

ARG

ASP

SER

GLU

HIS

GLU

GLY

HIS

8

LYS

VAL

CYS

THR

SER

CYS

GLU

GLY

ASN

9

ILE

CYS

ASN

LEU

PRO

LEU

PRO

ARG

ASN

GLU

10

THR

ASP

ALA

THR

PHE

ALA

Samples:

sample_1: Lypd6sh, [U-99% 13C; U-99% 15N], 0.1 mM

sample_2: Lypd6sh, [U-99% 15N], 0.1 mM

sample_conditions_1: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1

Software:

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

TOPSPIN v3.97, Bruker Biospin - collection

CARA, Keller and Wuthrich - chemical shift assignment

NMR spectrometers:

Bruker AvanceIII 800 MHz
Bruker AvanceIII 600 MHz

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