BMRB Entry 17358

Name: Solution structure of the third Immunoglobulin-like domain of nectin-1
Published: 2012-02-15

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PDB ID: 2l7j
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17358
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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 third Immunoglobulin-like domain of nectin-1

Deposition date:

2010-12-13

Original release date:

2012-02-15

Authors:

Clausen, Ole; Poulsen, Flemming

Citation:

Citation: Clausen, Ole; Poulsen, Flemming. "Solution structure of the third Immunoglobulin-like domain of nectin-1" .

Assembly members:

Assembly members:
entity, polymer, 95 residues, 10599.844 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Pichia pastoris Vector: pPICZalpha

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: LNVQYEPEVTIEGFDGNWYL QRTDVKLTCKADANPPATEY HWTTLNGSLPKGVEAQNRTL FFRGPITYSLAGTYICEATN PIGTRSGQVEVNITH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	170
15N chemical shifts	84
1H chemical shifts	373

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	nectin-1	1

Entities:

Entity 1, nectin-1 95 residues - 10599.844 Da.

1

LEU

ASN

VAL

GLN

TYR

GLU

PRO

GLU

VAL

THR

2

ILE

GLU

GLY

PHE

ASP

GLY

ASN

TRP

TYR

LEU

3

GLN

ARG

THR

ASP

VAL

LYS

LEU

THR

CYS

LYS

4

ALA

ASP

ALA

ASN

PRO

ALA

THR

GLU

TYR

5

HIS

TRP

THR

LEU

ASN

GLY

SER

LEU

PRO

6

LYS

GLY

VAL

GLU

ALA

GLN

ASN

ARG

THR

LEU

7

PHE

ARG

GLY

PRO

ILE

THR

TYR

SER

LEU

8

ALA

GLY

THR

TYR

ILE

CYS

GLU

ALA

THR

ASN

9

PRO

ILE

GLY

THR

ARG

SER

GLY

GLN

VAL

GLU

10

VAL

ASN

ILE

THR

HIS

Samples:

sample_1: nectin-1, [U-13C; U-15N], 1.0 mM; sodium phosphate 10 mM; sodium chloride 50 mM; sodium azide 0.02 % v/v

sample_conditions_1: ionic strength: 0.06 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

VNMR, Varian - collection

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

PRONTO, Kjur, Andersen and Poulsen - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

ARIA, Linge, O'Donoghue and Nilges - refinement

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

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Varian INOVA 750 MHz

PDB	2L7J
GB	AAF60333 AAF76195 AAG22808 AAG30283 AAH60694
REF	NP_001093946 NP_067399 XP_003513871 XP_004667415 XP_005069470
SP	Q9JKF6
AlphaFold	Q9JKF6