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- PDB-2p01: The structure of receptor-associated protein(RAP) -

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Basic information

Entry
Database: PDB / ID: 2p01
TitleThe structure of receptor-associated protein(RAP)
ComponentsAlpha-2-macroglobulin receptor-associated protein
KeywordsCELL ADHESION / receptor-associated protein / RAP
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 / SANS measurement
AuthorsLee, D. / Walsh, J.D. / Migliorini, M. / Yu, P. / Cai, T. / Schwieters, C.D. / Krueger, S. / Strickland, D.K. / Wang, Y.X.
CitationJournal: Protein Sci. / Year: 2007
Title: The structure of receptor-associated protein (RAP).
Authors: Lee, D. / Walsh, J.D. / Migliorini, M. / Yu, P. / Cai, T. / Schwieters, C.D. / Krueger, S. / Strickland, D.K. / Wang, Y.X.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 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


Theoretical massNumber of molelcules
Total (without water)37,8501
Polymers37,8501
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 least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 37849.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30533

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
NMR detailsText: SANS measurement

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Sample preparation

Sample conditionsIonic strength: 75 mM NaPi 50 mM NaCl / pH: 7.25 / Pressure: AMBIENT / Temperature: 303 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
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2P.GUNTERT ET AL.structure solution
X-PLOR3refinement
RefinementMethod: SANS measurement / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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