BMRB Entry 30042

Name: Murin CXCL13 solution structure featuring a folded N-terminal domain
Published: 2017-03-30

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PDB ID: 5izb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30042
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Murin CXCL13 solution structure featuring a folded N-terminal domain PubMed: 29070611

Deposition date: 2016-03-25 Original release date: 2017-03-30

Authors: Monneau, Y.; Lortat-Jacob, H.

Citation: Monneau, Yoan; Luo, Lingjie; Sankaranarayanan, Nehru Viji; Nagarajan, Balaji; Vives, Romain; Baleux, Francoise; Desai, Umesh; Arenzana-Seidedos, Fernando; Lortat-Jacob, Hugues. "Solution structure of CXCL13 and heparan sulfate binding show that GAG binding site and cellular signalling rely on distinct domains" Open Biol. 7, 170133-170133 (2017).

Assembly members:
entity_1, polymer, 89 residues, 9938.868 Da.

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

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):
entity_1: MILEAHYTNLKCRCSGVIST VVGLNIIDRIQVTPPGNGCP KTEVVIWTKMKKVICVNPRA KWLQRLLRHVQSKSLSSTPQ APVSKRRAA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	309
15N chemical shifts	91
1H chemical shifts	647

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 89 residues - 9938.868 Da.

1

MET

ILE

LEU

GLU

ALA

HIS

TYR

THR

ASN

LEU

2

LYS

CYS

ARG

CYS

SER

GLY

VAL

ILE

SER

THR

3

VAL

GLY

LEU

ASN

ILE

ASP

ARG

ILE

4

GLN

VAL

THR

PRO

GLY

ASN

GLY

CYS

PRO

5

LYS

THR

GLU

VAL

ILE

TRP

THR

LYS

MET

6

LYS

VAL

ILE

CYS

VAL

ASN

PRO

ARG

ALA

7

LYS

TRP

LEU

GLN

ARG

LEU

ARG

HIS

VAL

8

GLN

SER

LYS

SER

LEU

SER

THR

PRO

GLN

9

ALA

PRO

VAL

SER

LYS

ARG

ALA

Samples:

sample_1: CXCL13, [U-15N], 850 uM; potassium phosphate 20 mM; NaCl 100 mM

sample_2: CXCL13, [U-13C; U-15N], 280 uM; potassium phosphate 20 mM; NaCl 100 mM

sample_3: CXCL13, [U-13C; U-15N], 280 uM; potassium phosphate 20 mM; NaCl 100 mM

sample_4: CXCL13, [U-10% 13C; U-100% 15N], 280 uM; potassium phosphate 20 mM; NaCl 100 mM

sample_conditions_1: ionic strength: 120 mM; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-edited NOESY	sample_1	isotropic	sample_conditions_1
3D 13C-edited NOESY	sample_2	isotropic	sample_conditions_1
3D 13C-HMQC-NOESY-13C,1H-HMQC	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_3	isotropic	sample_conditions_1
3D HNCA	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_3	isotropic	sample_conditions_1
3D HACACO	sample_3	isotropic	sample_conditions_1
3D H(C)CH-TOCSY	sample_3	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC aliphatic	sample_4	isotropic	sample_conditions_1
2D COSYdqf	sample_4	isotropic	sample_conditions_1
2D TOCSY	sample_4	isotropic	sample_conditions_1
2D CBCGCDHD	sample_2	isotropic	sample_conditions_1
3D HNCOCA	sample_3	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMRFAM-SPARKY, Lee et al. Bioinformatics 2015 Apr 15; 31(8):1325-7 - chemical shift assignment

cyana, Guntert, P., Mumenthaler, C., & Wuthrich, K., Herrmann, T., - structure calculation

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 700 MHz
Bruker AvanceIII 950 MHz
Bruker AvanceIII 850 MHz

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