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- PDB-1nre: RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, MINIMIZED AVERAG... -

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Basic information

Entry
Database: PDB / ID: 1nre
TitleRECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsRECEPTOR-ASSOCIATED PROTEIN
KeywordsCELL SURFACE PROTEIN / ALPHA2MACROGLOBULIN RECEPTOR ASSOCIATED PROTEIN / LOW DENSITY LIPOPROTEIN RECEPTOR FAMILY ASSOCIATED PROTEIN / LDLR FAMILY ASSOCIATED PROTEIN / HELIX BUNDLE
Function / homology
Function and homology information


extracellular negative regulation of signal transduction / regulation of receptor-mediated endocytosis / negative regulation of very-low-density lipoprotein particle clearance / rough endoplasmic reticulum lumen / lipase binding / 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 / regulation of receptor-mediated endocytosis / negative regulation of very-low-density lipoprotein particle clearance / rough endoplasmic reticulum lumen / lipase binding / 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 / negative regulation of protein binding / endomembrane system / endosome lumen / Golgi lumen / heparin binding / amyloid-beta binding / endosome / receptor ligand activity / signaling receptor binding / cell surface / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular region / plasma membrane
Similarity search - Function
RAP domain / 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 / Receptor-associated Protein ...RAP domain / 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 / Receptor-associated Protein / 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 / DG, MD
AuthorsNielsen, P.R. / Poulsen, F.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The solution structure of the N-terminal domain of alpha2-macroglobulin receptor-associated protein.
Authors: Nielsen, P.R. / Ellgaard, L. / Etzerodt, M. / Thogersen, H.C. / Poulsen, F.M.
#1: Journal: To be Published
Title: Alpha2-Macroglobulin Receptor Associated Proteins Consist of Three Domains with Similar Structural Motifs. The 1H, 15N, and 13C Chemical Shift Assignments and Secondary Structure of the ...Title: Alpha2-Macroglobulin Receptor Associated Proteins Consist of Three Domains with Similar Structural Motifs. The 1H, 15N, and 13C Chemical Shift Assignments and Secondary Structure of the Truncated N-Terminal Domain of Human RAP
Authors: Nielsen, P.R. / Ellgaard, L. / Jensen, P.H. / Thoegersen, H.C. / Poulsen, F.M.
#2: Journal: Eur.J.Biochem. / Year: 1997
Title: Dissection of the Domain Architecture of the Alpha2Macroglobulin-Receptor-Associated Protein
Authors: Ellgaard, L. / Holtet, T.L. / Nielsen, P.R. / Etzerodt, M. / Gliemann, J. / Thogersen, H.C.
History
DepositionMay 8, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: RECEPTOR-ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,5361
Polymers9,5361
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 / 100LOWEST ENERGY
Representative

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Components

#1: Protein RECEPTOR-ASSOCIATED PROTEIN / RAP / LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN / ALPHA=2=MACROGLOBULIN RECEPTOR ASSOCIATED PROTEIN


Mass: 9536.008 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, DOMAIN 1, RESIDUES 17 - 97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PT=7=H=6=UB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P30533

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.4 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DG, MD / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 1

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