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- PDB-2l9l: NMR Structure of the Mouse MFG-E8 C2 Domain -

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Basic information

Entry
Database: PDB / ID: 2l9l
TitleNMR Structure of the Mouse MFG-E8 C2 Domain
ComponentsLactadherinMFGE8
KeywordsAPOPTOSIS / PHOSPHATIDYLSERINE-BINDING PROTEIN
Function / homology
Function and homology information


Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / phagocytosis, recognition / phosphatidylethanolamine binding / apoptotic cell clearance / phagocytosis, engulfment / extrinsic component of plasma membrane / phosphatidylserine binding / single fertilization / positive regulation of phagocytosis ...Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / phagocytosis, recognition / phosphatidylethanolamine binding / apoptotic cell clearance / phagocytosis, engulfment / extrinsic component of plasma membrane / phosphatidylserine binding / single fertilization / positive regulation of phagocytosis / integrin binding / angiogenesis / collagen-containing extracellular matrix / cell adhesion / external side of plasma membrane / extracellular space
Similarity search - Function
: / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / EGF-like domain / Galactose-binding domain-like / Epidermal growth factor-like domain. ...: / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / EGF-like domain / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYe, H. / Yoon, H.S.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: NMR solution structure of C2 domain of MFG-E8 and insights into its molecular recognition with phosphatidylserine
Authors: Ye, H. / Li, B. / Subramanian, V. / Choi, B.H. / Liang, Y. / Harikishore, A. / Chakraborty, G. / Baek, K. / Yoon, H.S.
History
DepositionFeb 21, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references / Other
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactadherin


Theoretical massNumber of molelcules
Total (without water)19,4381
Polymers19,4381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lactadherin / MFGE8 / MFGM / Milk fat globule-EGF factor 8 / MFG-E8 / SED1 / Sperm surface protein SP47 / MP47


Mass: 19437.758 Da / Num. of mol.: 1 / Fragment: C2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mfge8 / Production host: Escherichia coli (E. coli) / References: UniProt: P21956

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCA
1513D HNCO
1613D H(CC)(CO)NH
1713D (H)CC(CO)NH
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11123D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate-1, 20 mM sodium chloride-2, 0.01 % sodium azide-3, 0.8 mM [U-13C; U-15N] MFG-E8 C2 domain-4, 90% H2O/10% D2O90% H2O/10% D2O
220 mM sodium phosphate-5, 20 mM sodium chloride-6, 0.01 % sodium azide-7, 0.8 mM [U-13C; U-15N] MFG-E8 C2 domain-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
20 mMsodium chloride-21
0.01 %sodium azide-31
0.8 mMMFG-E8 C2 domain-4[U-13C; U-15N]1
20 mMsodium phosphate-52
20 mMsodium chloride-62
0.01 %sodium azide-72
0.8 mMMFG-E8 C2 domain-8[U-13C; U-15N]2
Sample conditionsIonic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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