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- PDB-1ov2: Ensemble of the solution structures of domain one of receptor ass... -

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Basic information

Entry
Database: PDB / ID: 1ov2
TitleEnsemble of the solution structures of domain one of receptor associated protein
ComponentsAlpha-2-macroglobulin receptor-associated protein precursor
KeywordsReceptor Associated Protein / Helical protein
Function / homology
Function and homology information


extracellular negative regulation of signal transduction / lipase binding / negative regulation of very-low-density lipoprotein particle clearance / regulation of receptor-mediated endocytosis / rough endoplasmic reticulum lumen / receptor antagonist activity / amyloid-beta clearance by transcytosis / negative regulation of amyloid-beta clearance / very-low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta clearance ...extracellular negative regulation of signal transduction / lipase binding / negative regulation of very-low-density lipoprotein particle clearance / regulation of receptor-mediated endocytosis / rough endoplasmic reticulum lumen / receptor antagonist activity / amyloid-beta clearance by transcytosis / negative regulation of amyloid-beta clearance / very-low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta clearance / cis-Golgi network / negative regulation of receptor internalization / low-density lipoprotein particle receptor binding / endoplasmic reticulum-Golgi intermediate compartment / endomembrane system / negative regulation of protein binding / endosome lumen / Golgi lumen / heparin binding / amyloid-beta binding / endosome / receptor ligand activity / signaling receptor binding / Golgi apparatus / cell surface / signal transduction / endoplasmic reticulum / extracellular region / plasma membrane
Similarity search - Function
RAP domain / Receptor-associated Protein / Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain ...RAP domain / Receptor-associated Protein / Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / Endoplasmic reticulum targeting sequence. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-2-macroglobulin receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsiona angle dynamics, simulated anealing
AuthorsWu, Y. / Migliorini, M. / Yu, P. / Strickland, D.K. / Wang, Y.X.
CitationJournal: J.Biomol.Nmr / Year: 2003
Title: 1H, 13C and 15N resonance assignments of domain 1 of receptor associated protein.
Authors: Wu, Y. / Migliorini, M. / Yu, P. / Strickland, D.K. / Wang, Y.X.
History
DepositionMar 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-2-macroglobulin receptor-associated protein precursor


Theoretical massNumber of molelcules
Total (without water)11,6811
Polymers11,6811
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)39 / 60structures with the least restraint violations
RepresentativeModel #1closest to the average,minimized average structure

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Components

#1: Protein Alpha-2-macroglobulin receptor-associated protein precursor / Alpha-2-MRAP / Low density lipoprotein receptor-related protein- associated protein 1 / RAP


Mass: 11681.404 Da / Num. of mol.: 1 / Fragment: domain 1 of receptor associated protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRPAP1 OR A2MRAP / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P30533

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
1414D 13C/15N-separated NOESY

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Sample preparation

DetailsContents: ~1.2 mM of 13C/15N isotope labeled domain 1 of receptor associated protein
Solvent system: 50 mM NaCl, 75 mM NaPi, pH 6.5
Sample conditionsIonic strength: 50 mM NaCl, 75 mM NaPi / pH: 6.5 / Pressure: ambient / Temperature: 303.5 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
xplor-nih1Schwieters, C.structure solution
NMRPipe1Delarglio, F.processing
interhlx1K. Yap, University of Toronto, Canandastructure solution
interhlx1K. Yap, University of Toronto, Canandarefinement
RefinementMethod: torsiona angle dynamics, simulated anealing / Software ordinal: 1
Details: The structures were determined using multi-dimension hetero-nuclear NMR spectroscopy. The constraints consist of NOE, diheadral, J-coupling, chemical shift, conformational data base as well ...Details: The structures were determined using multi-dimension hetero-nuclear NMR spectroscopy. The constraints consist of NOE, diheadral, J-coupling, chemical shift, conformational data base as well as two setsof dipolar couplings measured from two different alignment media.
NMR representativeSelection criteria: closest to the average,minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 39

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