BMRB Entry 18816

Name: Solution structure of the tenth complement type repeat of human megalin
Published: 2013-01-07

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PDB ID: 2m0p
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18816
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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:

Solution structure of the tenth complement type repeat of human megalin

Deposition date:

2012-11-01

Original release date:

2013-01-07

Authors:

Dagil, Robert; Kragelund, Birthe

Citation:

Citation: Dagil, Robert; Nykjaer, Charlotte; Bonvin, Anders; Kragelund, Alexandre M J J. "Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin." J. Biol. Chem. 288, 4424-4435 (2013).
PubMed: 23275343

Assembly members:

Assembly members:
CR10, polymer, 52 residues, 5045.292 Da.
CALCIUM ION, non-polymer, 40.078 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Pichia pastoris Vector: pPICaC

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CR10: THAPASCLDTQYTCDNHQCI SKNWVCDTDNDCGDGSDEKN CNSTETHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	164
15N chemical shifts	44
1H chemical shifts	243

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CR10	1
2	Calcium ion	2

Entities:

Entity 1, CR10 52 residues - 5045.292 Da.

1

THR

HIS

ALA

PRO

ALA

SER

CYS

LEU

ASP

THR

2

GLN

TYR

THR

CYS

ASP

ASN

HIS

GLN

CYS

ILE

3

SER

LYS

ASN

TRP

VAL

CYS

ASP

THR

ASP

ASN

4

ASP

CYS

GLY

ASP

GLY

SER

ASP

GLU

LYS

ASN

5

CYS

ASN

SER

THR

GLU

THR

HIS

6

HIS

Entity 2, Calcium ion - Ca - 40.078 Da.

1

CA

Samples:

sample_1: CR10, [U-100% 13C; U-100% 15N], 0.6 mM; sodium chloride 100 mM; calcium chloride 50 mM; TRIS 50 mM; DSS 0.1 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_2: CR10, [U-100% 13C; U-100% 15N], 0.6 mM; calcium chloride 50 mM; sodium chloride 100 mM; TRIS 50 mM; DSS 0.1 mM; sodium azide 0.1%; D2O 100%

sample_conditions_1: ionic strength: 0.2 M; pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1

Software:

Analysis v2.2, CCPN - chemical shift assignment, peak picking

ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution

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

NMR spectrometers:

Varian INOVA 750 MHz
Varian INOVA 800 MHz
Bruker Avance 800 MHz