BMRB Entry 18596

Name: Solution structure of a Eosinophil Cationic Protein-trisaccharide heparin mimetic complex
Published: 2013-07-29

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PDB ID: 2lvz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18596
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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 a Eosinophil Cationic Protein-trisaccharide heparin mimetic complex

Deposition date:

2012-07-17

Original release date:

2013-07-29

Authors:

Garcia Mayoral, Maria Flor; Canales, Angeles; Diaz, Dolores; Lopez Prados, Javier; Moussaoui, Mohammed; de Paz, Jose Luis; Angulo, Jesus; Nieto, Pedro Manuel; Jimenez Barbero, Jesus; Boix, Ester; Bruix, Marta

Citation:

Citation: Garcia Mayoral, Maria Flor; Canales, Angeles; Diaz, Dolores; Lopez Prados, Javier; Moussaoui, Mohammed; de Paz, Jose Luis; Angulo, Jesus; Nieto, Pedro Manuel; Jimenez Barbero, Jesus; Boix, Ester; Bruix, Marta. "Insights into the glycosaminoglycan-mediated cytotoxic mechanism of eosinophil cationic protein revealed by NMR" ACS Chem. Biol. 8, 144-151 (2013).
PubMed: 23025322

Assembly members:

Assembly members:
Eosinophil_Cationic_Protein, polymer, 133 residues, 15598.974 Da.
SUGAR_(3-MER), polymer, 3 residues, 595.473 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET11c

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Eosinophil_Cationic_Protein: RPPQFTRAQWFAIQHISLNP PRCTIAMRAINNYRWRCKNQ NTFLRTTFANVVNVCGNQSI RCPHNRTLNNCHRSRFRVPL LHCDLINPGAQNISNCRYAD RPGRRFYVVACDNRDPRDSP RYPVVPVHLDTTI
SUGAR_(3-MER): XXX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	410
15N chemical shifts	148
1H chemical shifts	923

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Eosinophil Cationic Protein	1
2	SUGAR (2-MER)	2

Entities:

Entity 1, Eosinophil Cationic Protein 133 residues - 15598.974 Da.

1

ARG

PRO

GLN

PHE

THR

ARG

ALA

GLN

TRP

2

PHE

ALA

ILE

GLN

HIS

ILE

SER

LEU

ASN

PRO

3

PRO

ARG

CYS

THR

ILE

ALA

MET

ARG

ALA

ILE

4

ASN

TYR

ARG

TRP

ARG

CYS

LYS

ASN

GLN

5

ASN

THR

PHE

LEU

ARG

THR

PHE

ALA

ASN

6

VAL

ASN

VAL

CYS

GLY

ASN

GLN

SER

ILE

7

ARG

CYS

PRO

HIS

ASN

ARG

THR

LEU

ASN

8

CYS

HIS

ARG

SER

ARG

PHE

ARG

VAL

PRO

LEU

9

LEU

HIS

CYS

ASP

LEU

ILE

ASN

PRO

GLY

ALA

10

GLN

ASN

ILE

SER

ASN

CYS

ARG

TYR

ALA

ASP

11

ARG

PRO

GLY

ARG

PHE

TYR

VAL

ALA

12

CYS

ASP

ASN

ARG

ASP

PRO

ARG

ASP

SER

PRO

13

ARG

TYR

PRO

VAL

PRO

VAL

HIS

LEU

ASP

14

THR

ILE

Entity 2, SUGAR (2-MER) 3 residues - 595.473 Da.

1

LVZ

IDS

SGN

Samples:

sample_1: Eosinophil_Cationic_Protein, [U-13C; U-15N], 0.5 mM; Heparin (3-MER) 0.5 mM; potassium phosphate 100 mM; potassium chloride 300 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.3 M; pH: 4.0; pressure: 1 atm; temperature: 273 K

Experiments:

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

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 800 MHz

BMRB	15757
PDB	1DYT 1H1H 1QMT 2KB5 2LVZ 4A2O 4A2Y 4OWZ 4OXB 4OXF
EMBL	CAA33251 CAA34545 CAA39462
GB	AAA50283 AAC50143 AAC50150 AAG09050 AAG09051
REF	NP_002926 XP_004054906 XP_004054907
SP	P12724 P47778 P47780
TPE	CDG31917 CDG31938
AlphaFold	P12724 P47778 P47780