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- PDB-2kgl: NMR solution structure of MESD -

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Basic information

Entry
Database: PDB / ID: 2kgl
TitleNMR solution structure of MESD
ComponentsMesoderm development candidate 2
KeywordsCHAPERONE / MESD / LRP5/6 / YWTD / Wnt
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
AuthorsChen, J. / Wang, J.
CitationJournal: Structure / Year: 2011
Title: Two Structural and Functional Domains of MESD Required for Proper Folding and Trafficking of LRP5/6.
Authors: Chen, J. / Liu, C.C. / Li, Q. / Nowak, C. / Bu, G. / Wang, J.
History
DepositionMar 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mesoderm development candidate 2


Theoretical massNumber of molelcules
Total (without water)22,0751
Polymers22,0751
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mesoderm development candidate 2


Mass: 22074.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mesdc2 / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ERE7

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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 HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1713D HCCTOCSY
1813D CCCTOCSY
1914D 13C/15N-edited NOESY

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Sample preparation

DetailsContents: 0.8-1.0 mM MESD, 25 mM sodium chloride, 10 mM EDTA, 10 mM DTT, 0.1 mM sodium azide, 25 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMMESD0.8-1.01
25 mMsodium chloride1
10 mMEDTA1
10 mMDTT1
0.1 mMsodium azide1
25 mMsodium phosphate1
Sample conditionspH: 6.8 / 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
NameVersionDeveloperClassification
NMRViewJohnson, B. et al.chemical shift assignment
CNS1.2Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1646 / NOE intraresidue total count: 171 / NOE long range total count: 397 / NOE medium range total count: 568 / NOE sequential total count: 510 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 132 / Protein psi angle constraints total count: 132
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2.53 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 6.61 ° / Maximum upper distance constraint violation: 0.28 Å / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.0062 Å / Distance rms dev error: 0.0013 Å

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