BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19783

Title: Solution structure of the fourth constant immunoglobulin domain of nurse shark IgNAR   PubMed: 24830426

Deposition date: 2014-02-10 Original release date: 2014-06-30

Authors: Hennig, Janosch; Sattler, Michael

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).

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

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

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

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

Data sets:
Data typeCount
13C chemical shifts394
15N chemical shifts97
1H chemical shifts704

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Fourth counstant immunoglobulin domain of IgNAR1

Entities:

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

1   METGLYARGGLNTHRASPILESERVALSER
2   LEULEULYSPROPROPHEGLUGLUILETRP
3   THRGLNGLNTHRALATHRILEVALCYSGLU
4   ILEVALTYRSERASPLEUGLUASNILELYS
5   VALPHETRPGLNVALASNGLYVALGLUARG
6   LYSLYSGLYVALGLUTHRGLNASNPROGLU
7   TRPSERGLYSERLYSSERTHRILEVALSER
8   LYSLEULYSVALMETALASERGLUTRPASP
9   SERGLYTHRGLUTYRVALCYSLEUVALGLU
10   ASPSERGLULEUPROTHRPROVALLYSALA
11   SERILEARGLYSALA

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_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, . - water refinement

NMR spectrometers:

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

Related Database Links:

PDB

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts