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- PDB-2kmi: MESD(12-155), The Core Structural Domain of MESD that Is Essentia... -

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Basic information

Entry
Database: PDB / ID: 2kmi
TitleMESD(12-155), The Core Structural Domain of MESD that Is Essential for Proper Folding of LRP5/6
ComponentsMesoderm development candidate 2
KeywordsCHAPERONE / MESD/Boca / LRP5/6
Function / homology
Function and homology information


positive regulation of skeletal muscle acetylcholine-gated channel clustering / protein localization to cell surface / low-density lipoprotein particle receptor binding / mesoderm development / positive regulation of Wnt signaling pathway / phagocytosis / protein folding chaperone / ossification / protein localization to plasma membrane / Wnt signaling pathway ...positive regulation of skeletal muscle acetylcholine-gated channel clustering / protein localization to cell surface / low-density lipoprotein particle receptor binding / mesoderm development / positive regulation of Wnt signaling pathway / phagocytosis / protein folding chaperone / ossification / protein localization to plasma membrane / Wnt signaling pathway / protein folding / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
LRP chaperone MESD / Chaperone for wingless signalling and trafficking of LDL receptor
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChen, J. / Wang, J.
Citation
Journal: J.Biomol.Nmr / Year: 2010
Title: NMR structure note: solution structure of the core domain of MESD that is essential for proper folding of LRP5/6.
Authors: Chen, J. / Li, Q. / Liu, C.C. / Zhou, B. / Bu, G. / Wang, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Coaxing the LDL receptor family into the fold
Authors: Herz, J. / Marschang, P.
History
DepositionJul 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Mesoderm development candidate 2


Theoretical massNumber of molelcules
Total (without water)16,6931
Polymers16,6931
Non-polymers00
Water00
1


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

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Components

#1: Protein Mesoderm development candidate 2


Mass: 16692.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mesdc2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ERE7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Mesoderm development (MESD) protein is a 195-residue protein that serves as a specialized molecular chaperone to promote the proper folding of the six-bladed ??-propeller/EGF modules of the ...Details: Mesoderm development (MESD) protein is a 195-residue protein that serves as a specialized molecular chaperone to promote the proper folding of the six-bladed ??-propeller/EGF modules of the LDL receptor family members, and Mesd(12-155) is the most conserved region of Mesd protein.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1.0 mM [U-13C; U-15N] mesd12-155, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: mesd12-155-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionspH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
PIPPGarrettchemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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