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- PDB-1op1: Solution NMR structure of domain 1 of receptor associated protein -

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Basic information

Entry
Database: PDB / ID: 1op1
TitleSolution NMR structure of domain 1 of receptor associated protein
ComponentsAlpha-2-macroglobulin receptor-associated protein precursor
KeywordsReceptor Associated Protein / helical bundle
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 / receptor ligand activity / endosome / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / signal transduction / 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 / torsion angle dynamics, simulated annealing protocol
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 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Database references / Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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)9,6641
Polymers9,6641
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)1 / -
Representative

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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: 9664.136 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 / Production host: Escherichia coli (E. coli) / Strain (production host): pGex-2T / 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
1214D 13C/15N-separated NOESY
2323D 13C-separated NOESY
141HNHA
NMR detailsText: The structure was determined using multi-dimensionm hetero-nuclear NMR spectroscopy. The constraints consists of NOE, dihedral, J-coupling, chemical shift, conformational database as well as ...Text: The structure was determined using multi-dimensionm hetero-nuclear NMR spectroscopy. The constraints consists of NOE, dihedral, J-coupling, chemical shift, conformational database as well as two sets of dipolar couplings measured from two different alignment media.

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Sample preparation

Details
Solution-IDContentsSolvent system
1~1.2 mM 15N/13C isotope labeled D1 of RAP in a 50 mM NaCl, 75 mM NaPi, pH 6.595% H2O and 5% D2O
2~1.2 mM 15N/13C isotpe-labeled D1 of RAP in a 50 mM NaCl, 75 mM NaPi, pH 6.599.99% D2O
Sample conditionsIonic strength: 50 mM NaCl, 75 mM NaPi / pH: 6.5 / Pressure: ambient / Temperature: 303.5 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
nih-xplor1.0.6~1.2 mM D1 of RAP in a 50 mM~1.2 mM D1 ~1.2 mM D1 of RAP inSchwieters, C. D., Kuszewski, J., Tjandra, N. and Clore, G. M.refinement
NMRPipeDelaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J. and Bax, A.processing
NMRPipeGarrett, D. S., Powers, R., Gronenborn, A. M. and Clore, G. M.data analysis
interhlxK. Yap, University of Toronto, Canadastructure solution
RefinementMethod: torsion angle dynamics, simulated annealing protocol
Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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