[English] 日本語
Yorodumi
- PDB-2fyl: Haddock model of the complex between double module of LRP, CR56, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fyl
TitleHaddock model of the complex between double module of LRP, CR56, and first domain of receptor associated protein, RAP-d1.
Components
  • Alpha-2-macroglobulin receptor-associated protein
  • Low-density lipoprotein receptor-related protein 1
KeywordsSURFACE ACTIVE PROTEIN / Complex / shift-mapping / haddock / interface
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / : / positive regulation of lipid transport / extracellular negative regulation of signal transduction / positive regulation of transcytosis / lipoprotein particle receptor binding / regulation of receptor-mediated endocytosis / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / : / positive regulation of lipid transport / extracellular negative regulation of signal transduction / positive regulation of transcytosis / lipoprotein particle receptor binding / regulation of receptor-mediated endocytosis / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of very-low-density lipoprotein particle clearance / lipase binding / positive regulation of lysosomal protein catabolic process / rough endoplasmic reticulum lumen / regulation of cholesterol transport / aorta morphogenesis / receptor antagonist activity / amyloid-beta clearance by transcytosis / regulation of extracellular matrix disassembly / clathrin heavy chain binding / negative regulation of amyloid-beta clearance / negative regulation of smooth muscle cell migration / low-density lipoprotein particle receptor activity / amyloid-beta clearance by cellular catabolic process / very-low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta clearance / transcytosis / plasma membrane protein complex / cis-Golgi network / negative regulation of receptor internalization / heparan sulfate proteoglycan binding / astrocyte activation involved in immune response / apoptotic cell clearance / cargo receptor activity / lipoprotein transport / scavenger receptor activity / lysosomal transport / low-density lipoprotein particle receptor binding / enzyme-linked receptor protein signaling pathway / negative regulation of SMAD protein signal transduction / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of Wnt signaling pathway / positive regulation of endocytosis / microtubule organizing center / amyloid-beta clearance / apolipoprotein binding / positive regulation of cholesterol efflux / phagocytosis / Scavenging of heme from plasma / transport across blood-brain barrier / retinoid metabolic process / Retinoid metabolism and transport / clathrin-coated pit / negative regulation of protein binding / endomembrane system / receptor-mediated endocytosis / endosome lumen / positive regulation of protein localization to plasma membrane / regulation of actin cytoskeleton organization / receptor internalization / lipid metabolic process / Golgi lumen / cellular response to amyloid-beta / endocytic vesicle membrane / heparin binding / signaling receptor activity / amyloid-beta binding / basolateral plasma membrane / early endosome / receptor complex / endosome / receptor ligand activity / signaling receptor binding / lysosomal membrane / negative regulation of gene expression / focal adhesion / calcium ion binding / protein-containing complex binding / nucleolus / cell surface / endoplasmic reticulum / Golgi apparatus / signal transduction / RNA binding / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / 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 ...Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / 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 / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Endoplasmic reticulum targeting sequence. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-2-macroglobulin receptor-associated protein / Prolow-density lipoprotein receptor-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / HADDOCK modelling from chemical shift perturbation data on both complex partners
AuthorsJensen, G.A. / Andersen, O.M. / Bonvin, A.M. / Bjerrum-Bohr, I. / Etzerodt, M. / O'shea, C. / Poulsen, F.M. / Kragelund, B.B.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Binding Site Structure of One LRP-RAP Complex:Implications for a Common Ligand-Receptor Binding Motif.
Authors: Jensen, G.A. / Andersen, O.M. / Bonvin, A.M. / Bjerrum-Bohr, I. / Etzerodt, M. / O'shea, C. / Poulsen, F.M. / Kragelund, B.B.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-2-macroglobulin receptor-associated protein
B: Low-density lipoprotein receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5614
Polymers18,4812
Non-polymers802
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 / 200Best averaged HADDOCK score
RepresentativeModel #5lowest energy

-
Components

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


Mass: 9536.008 Da / Num. of mol.: 1 / Fragment: Rapd1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRPAP1, A2MRAP / Production host: Escherichia coli (E. coli) / References: UniProt: P30533
#2: Protein Low-density lipoprotein receptor-related protein 1 / LRP / Alpha-2-macroglobulin receptor


Mass: 8944.620 Da / Num. of mol.: 1 / Fragment: CR56
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07954
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111Exchange 15N,1H-HSQC
222Exchange 15N,1H,-HSQC
13115N,1H-HSQC
24215N,1H-HSQC
353HNCA
363HN(CA)CB, HN(CO)CACB

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.1mM [U-99% 15N]-CR56; 0.1mM RAPd1; H2O/D2O (90:10)H2O/D2O (90:10)
20.5mM [U-99% 15N]-RAPd1; 0.5mM CR56; H2O/D2O (90:10)H2O/D2O (90:10)
30.08 mM [U-99% 15N, U-99% 13C]-CR56; 0.08 mM [U-99% 15N, U-99% 13C]-RAPd1; H2O/D2O (90:10)H2O/D2O (90:10)
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameVersionDeveloperClassification
Pronto3D20020517Kjaer et aldata analysis
HADDOCKBonvin et alstructure solution
HADDOCKBonvin et alrefinement
RefinementMethod: HADDOCK modelling from chemical shift perturbation data on both complex partners
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Best averaged HADDOCK score / Conformers calculated total number: 200 / Conformers submitted total number: 1

+
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