[English] 日本語
Yorodumi
- PDB-1lre: RECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, 20 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lre
TitleRECEPTOR ASSOCIATED PROTEIN (RAP) DOMAIN 1, NMR, 20 STRUCTURES
ComponentsRECEPTOR-ASSOCIATED PROTEIN
KeywordsCELL SURFACE PROTEIN / ALPHA2-MACROGLOBULIN 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)20 / 100LOWEST ENERGY
Representative

-
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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

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

-
NMR measurement

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

-
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: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more