BMRB Entry 34176

Name: NMR solution structure of murine CXCL12 gamma isoform
Published: 2018-10-02

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PDB ID: 6ehz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34176
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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:

NMR solution structure of murine CXCL12 gamma isoform

Deposition date:

2017-09-15

Original release date:

2018-10-02

Authors:

Laguri, C.; Lortat-Jacob, H.; SImorre, J.

Citation:

Citation: Prechoux, Aurelie; Simorre, Jean-Pierre; Lortat-Jacob, Hugues; Laguri, Cedric. "Deciphering the structural attributes of protein-heparan sulfate interactions using chemo-enzymatic approaches and NMR spectroscopy" Glycobiology 31, 851-858 (2021).
PubMed: 33554262

Assembly members:

Assembly members:
entity_1, polymer, 98 residues, 11611.919 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: KPVSLSYRCPCRFFESHIAR ANVKHLKILNTPNCALQIVA RLKNNNRQVCIDPKLKWIQE YLEKALNKGRREEKVGKKEK IGKKKRQKKRKAAQKRKN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	373
15N chemical shifts	103
1H chemical shifts	545

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 98 residues - 11611.919 Da.

1

LYS

PRO

VAL

SER

LEU

SER

TYR

ARG

CYS

PRO

2

CYS

ARG

PHE

GLU

SER

HIS

ILE

ALA

ARG

3

ALA

ASN

VAL

LYS

HIS

LEU

LYS

ILE

LEU

ASN

4

THR

PRO

ASN

CYS

ALA

LEU

GLN

ILE

VAL

ALA

5

ARG

LEU

LYS

ASN

ARG

GLN

VAL

CYS

6

ILE

ASP

PRO

LYS

LEU

LYS

TRP

ILE

GLN

GLU

7

TYR

LEU

GLU

LYS

ALA

LEU

ASN

LYS

GLY

ARG

8

ARG

GLU

LYS

VAL

GLY

LYS

GLU

LYS

9

ILE

GLY

LYS

ARG

GLN

LYS

ARG

10

LYS

ALA

GLN

LYS

ARG

LYS

ASN

Samples:

sample_1: CXCL12 gamma isoform, [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; Na Phosphate buffer 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 5.7; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY methyls	sample_1	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CNS, Brunger A. T. et.al. - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - peak picking

CcpNMR, CCPN - chemical shift assignment

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

NMR spectrometers:

Varian 600 Direct Drive 600 MHz

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