BMRB Entry 17477

Name: NMR Structure of the Mouse MFG-E8 C2 Domain
Published: 2012-08-31

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PDB ID: 2l9l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17477
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of the Mouse MFG-E8 C2 Domain

Deposition date:

2011-02-21

Original release date:

2012-08-31

Authors:

Ye, Hong; Subramanian, Vivekanandan; Yu, Liang; Yoon, Ho Sup

Citation:

Citation: Ye, Hong; Li, Baihong; Subramanian, Vivekanandan; Choi, Bo-Hwa; Yu, Liang; Harikishore, Amaravadhi; Harikishore, Amaravadhi; Chakraborty, Goutam; Baek, Kwanghee; Yoon, Ho Sup. "NMR solution structure of C2 domain of MFG-E8 and insights into its molecular recognition with phosphatidylserine" Biochim. Biophys. Acta 1828, 1083-1093 (2013).
PubMed: 23262193

Assembly members:

Assembly members:
MFG-E8_C2_domain, polymer, 170 residues, 18609.027 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET29b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MFG-E8_C2_domain: MKSGHGCSEPLGLKNNTIPD SQMSASSSYKTWNLRAFGWY PHLGRLDNQGKINAWTAQSN SAKEWLQVDLGTQRQVTGII TQGARDFGHIQYVASYKVAH SDDGVQWTVYEEQGSSKVFQ GNLDNNSHKKNIFEKPFMAR YVRVLPVSWHNRITLRLELL GCLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	573
15N chemical shifts	160
1H chemical shifts	973

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MFG-E8_C2_domain	1

Entities:

Entity 1, MFG-E8_C2_domain 170 residues - 18609.027 Da.

1	MET	LYS	SER	GLY	HIS	GLY	CYS	SER	GLU	PRO
2	LEU	GLY	LEU	LYS	ASN	ASN	THR	ILE	PRO	ASP
3	SER	GLN	MET	SER	ALA	SER	SER	SER	TYR	LYS
4	THR	TRP	ASN	LEU	ARG	ALA	PHE	GLY	TRP	TYR
5	PRO	HIS	LEU	GLY	ARG	LEU	ASP	ASN	GLN	GLY
6	LYS	ILE	ASN	ALA	TRP	THR	ALA	GLN	SER	ASN
7	SER	ALA	LYS	GLU	TRP	LEU	GLN	VAL	ASP	LEU
8	GLY	THR	GLN	ARG	GLN	VAL	THR	GLY	ILE	ILE
9	THR	GLN	GLY	ALA	ARG	ASP	PHE	GLY	HIS	ILE
10	GLN	TYR	VAL	ALA	SER	TYR	LYS	VAL	ALA	HIS
11	SER	ASP	ASP	GLY	VAL	GLN	TRP	THR	VAL	TYR
12	GLU	GLU	GLN	GLY	SER	SER	LYS	VAL	PHE	GLN
13	GLY	ASN	LEU	ASP	ASN	ASN	SER	HIS	LYS	LYS
14	ASN	ILE	PHE	GLU	LYS	PRO	PHE	MET	ALA	ARG
15	TYR	VAL	ARG	VAL	LEU	PRO	VAL	SER	TRP	HIS
16	ASN	ARG	ILE	THR	LEU	ARG	LEU	GLU	LEU	LEU
17	GLY	CYS	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

Samples:

sample_1: sodium phosphate 20 mM; sodium chloride 20 mM; sodium azide 0.01%; MFG-E8 C2 domain, [U-13C; U-15N], 0.8 mM; H2O 90%; D2O 10%

sample_2: sodium phosphate 20 mM; sodium chloride 20 mM; sodium azide 0.01%; MFG-E8 C2 domain, [U-13C; U-15N], 0.8 mM; D2O 100%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 700 MHz

1	MET	LYS	SER	GLY	HIS	GLY	CYS	SER	GLU	PRO
2	LEU	GLY	LEU	LYS	ASN	ASN	THR	ILE	PRO	ASP
3	SER	GLN	MET	SER	ALA	SER	SER	SER	TYR	LYS
4	THR	TRP	ASN	LEU	ARG	ALA	PHE	GLY	TRP	TYR
5	PRO	HIS	LEU	GLY	ARG	LEU	ASP	ASN	GLN	GLY
6	LYS	ILE	ASN	ALA	TRP	THR	ALA	GLN	SER	ASN
7	SER	ALA	LYS	GLU	TRP	LEU	GLN	VAL	ASP	LEU
8	GLY	THR	GLN	ARG	GLN	VAL	THR	GLY	ILE	ILE
9	THR	GLN	GLY	ALA	ARG	ASP	PHE	GLY	HIS	ILE
10	GLN	TYR	VAL	ALA	SER	TYR	LYS	VAL	ALA	HIS
11	SER	ASP	ASP	GLY	VAL	GLN	TRP	THR	VAL	TYR
12	GLU	GLU	GLN	GLY	SER	SER	LYS	VAL	PHE	GLN
13	GLY	ASN	LEU	ASP	ASN	ASN	SER	HIS	LYS	LYS
14	ASN	ILE	PHE	GLU	LYS	PRO	PHE	MET	ALA	ARG
15	TYR	VAL	ARG	VAL	LEU	PRO	VAL	SER	TRP	HIS
16	ASN	ARG	ILE	THR	LEU	ARG	LEU	GLU	LEU	LEU
17	GLY	CYS	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

1	MET	LYS	SER	GLY	HIS	GLY	CYS	SER	GLU	PRO
2	LEU	GLY	LEU	LYS	ASN	ASN	THR	ILE	PRO	ASP
3	SER	GLN	MET	SER	ALA	SER	SER	SER	TYR	LYS
4	THR	TRP	ASN	LEU	ARG	ALA	PHE	GLY	TRP	TYR
5	PRO	HIS	LEU	GLY	ARG	LEU	ASP	ASN	GLN	GLY
6	LYS	ILE	ASN	ALA	TRP	THR	ALA	GLN	SER	ASN
7	SER	ALA	LYS	GLU	TRP	LEU	GLN	VAL	ASP	LEU
8	GLY	THR	GLN	ARG	GLN	VAL	THR	GLY	ILE	ILE
9	THR	GLN	GLY	ALA	ARG	ASP	PHE	GLY	HIS	ILE
10	GLN	TYR	VAL	ALA	SER	TYR	LYS	VAL	ALA	HIS
11	SER	ASP	ASP	GLY	VAL	GLN	TRP	THR	VAL	TYR
12	GLU	GLU	GLN	GLY	SER	SER	LYS	VAL	PHE	GLN
13	GLY	ASN	LEU	ASP	ASN	ASN	SER	HIS	LYS	LYS
14	ASN	ILE	PHE	GLU	LYS	PRO	PHE	MET	ALA	ARG
15	TYR	VAL	ARG	VAL	LEU	PRO	VAL	SER	TRP	HIS
16	ASN	ARG	ILE	THR	LEU	ARG	LEU	GLU	LEU	LEU
17	GLY	CYS	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS