BMRB Entry 19783

Name: Solution structure of the fourth constant immunoglobulin domain of nurse shark IgNAR
Published: 2014-06-30

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PDB ID: 2mkl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19783
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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 fourth constant immunoglobulin domain of nurse shark IgNAR

Deposition date:

2014-02-10

Original release date:

2014-06-30

Authors:

Hennig, Janosch; Sattler, Michael

Citation:

Citation: Feige, Matthias; Griwert, Melissa; Marcinowski, Moritz; Hennig, Janosch; Behnke, Julia; Auslinder, David; Herold, Eva; Peschek, Jirka; Castro, Caitlin; Flajnik, Martin; Hendershot, Linda; Sattler, Michael; Groll, Michael; Buchner, Johannes. "The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins" Proc. Natl. Acad. Sci. U.S.A. 111, 8155-8160 (2014).
PubMed: 24830426

Assembly members:

Assembly members:
entity, polymer, 105 residues, 11832.534 Da.

Natural source:

Natural source: Common Name: Nurse shark Taxonomy ID: 7801 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Ginglymostoma cirratum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MGRQTDISVSLLKPPFEEIW TQQTATIVCEIVYSDLENIK VFWQVNGVERKKGVETQNPE WSGSKSTIVSKLKVMASEWD SGTEYVCLVEDSELPTPVKA SIRKA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	394
15N chemical shifts	97
1H chemical shifts	704

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Fourth counstant immunoglobulin domain of IgNAR	1

Entities:

Entity 1, Fourth counstant immunoglobulin domain of IgNAR 105 residues - 11832.534 Da.

1

MET

GLY

ARG

GLN

THR

ASP

ILE

SER

VAL

SER

2

LEU

LYS

PRO

PHE

GLU

ILE

TRP

3

THR

GLN

THR

ALA

THR

ILE

VAL

CYS

GLU

4

ILE

VAL

TYR

SER

ASP

LEU

GLU

ASN

ILE

LYS

5

VAL

PHE

TRP

GLN

VAL

ASN

GLY

VAL

GLU

ARG

6

LYS

GLY

VAL

GLU

THR

GLN

ASN

PRO

GLU

7

TRP

SER

GLY

SER

LYS

SER

THR

ILE

VAL

SER

8

LYS

LEU

LYS

VAL

MET

ALA

SER

GLU

TRP

ASP

9

SER

GLY

THR

GLU

TYR

VAL

CYS

LEU

VAL

GLU

10

ASP

SER

GLU

LEU

PRO

THR

PRO

VAL

LYS

ALA

11

SER

ILE

ARG

LYS

ALA

Samples:

sample_1: Fourth counstant immunoglobulin domain of IgNAR, [U-100% 13C; U-100% 15N], 300 – 500 uM; sodium chloride 137 mM; potassium chloride 2.7 mM; sodium phosphate 10 mM; potassium phosphate 2 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_2: Fourth counstant immunoglobulin domain of IgNAR, [U-10% 13C], 300 – 500 uM; sodium chloride 137 mM; potassium chloride 2.7 mM; sodium phosphate 10 mM; potassium phosphate 2 mM; sodium azide 0.02%; sodium azide 90%; sodium azide 10%

sample_3: Fourth counstant immunoglobulin domain of IgNAR, [U-100% 13C; U-100% 15N], 300 – 500 uM; sodium chloride 137 mM; potassium chloride 2.7 mM; sodium phosphate 10 mM; potassium phosphate 2 mM; sodium azide 0.02%; Pf1 phage 10 mg/mL; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

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

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure calculation

ARIA, Linge, O'Donoghue and Nilges - water refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 750 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz