BMRB Entry 34005

Name: Murin CXCL13 solution structure
Published: 2017-06-15

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PDB ID: 5l7m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34005
MolProbity Validation Chart

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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:

Murin CXCL13 solution structure

Deposition date:

2016-06-03

Original release date:

2017-06-15

Authors:

Monneau, Y.; Lortat-Jacob, H.

Citation:

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).
PubMed: 29070611

Assembly members:

Assembly members:
entity_1, polymer, 88 residues, 9807.674 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: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: ILEAHYTNLKCRCSGVISTV VGLNIIDRIQVTPPGNGCPK TEVVIWTKMKKVICVNPRAK WLQRLLRHVQSKSLSSTPQA PVSKRRAA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	313
15N chemical shifts	81
1H chemical shifts	602

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 88 residues - 9807.674 Da.

1

ILE

LEU

GLU

ALA

HIS

TYR

THR

ASN

LEU

LYS

2

CYS

ARG

CYS

SER

GLY

VAL

ILE

SER

THR

VAL

3

VAL

GLY

LEU

ASN

ILE

ASP

ARG

ILE

GLN

4

VAL

THR

PRO

GLY

ASN

GLY

CYS

PRO

LYS

5

THR

GLU

VAL

ILE

TRP

THR

LYS

MET

LYS

6

LYS

VAL

ILE

CYS

VAL

ASN

PRO

ARG

ALA

LYS

7

TRP

LEU

GLN

ARG

LEU

ARG

HIS

VAL

GLN

8

SER

LYS

SER

LEU

SER

THR

PRO

GLN

ALA

9

PRO

VAL

SER

LYS

ARG

ALA

Samples:

sample_1: CXCL13, [U-15N], 850 uM

sample_2: CXCL13, [U-15N; U-13C], 560 uM

sample_3: CXCL13, [U-15N], 250 uM

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

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_2	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
3D H(C)CH-TOCSY	sample_2	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY-HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CG)(CD)HD	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY-HMQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

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

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

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

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