[English] 日本語
Yorodumi
- PDB-1cr8: LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN COMPLEMENT REPEAT 8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cr8
TitleLOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN COMPLEMENT REPEAT 8
ComponentsPROTEIN (LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN)
KeywordsLIPID BINDING PROTEIN / RECEPTOR / LIGAND BINDING / CALCIUM BINDING / LDLR / LRP
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / : / positive regulation of lipid transport / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of lysosomal protein catabolic process / regulation of cholesterol transport ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / : / positive regulation of lipid transport / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of lysosomal protein catabolic process / regulation of cholesterol transport / aorta morphogenesis / amyloid-beta clearance by transcytosis / regulation of extracellular matrix disassembly / clathrin heavy chain binding / negative regulation of smooth muscle cell migration / low-density lipoprotein particle receptor activity / amyloid-beta clearance by cellular catabolic process / plasma membrane protein complex / positive regulation of amyloid-beta clearance / transcytosis / heparan sulfate proteoglycan binding / astrocyte activation involved in immune response / apoptotic cell clearance / cargo receptor activity / lipoprotein transport / lysosomal transport / scavenger receptor activity / enzyme-linked receptor protein signaling pathway / negative regulation of SMAD protein signal transduction / negative regulation of Wnt signaling pathway / amyloid-beta clearance / microtubule organizing center / positive regulation of endocytosis / apolipoprotein binding / positive regulation of cholesterol efflux / phagocytosis / transport across blood-brain barrier / Scavenging of heme from plasma / retinoid metabolic process / Retinoid metabolism and transport / clathrin-coated pit / receptor-mediated endocytosis / positive regulation of protein localization to plasma membrane / regulation of actin cytoskeleton organization / receptor internalization / lipid metabolic process / cellular response to amyloid-beta / endocytic vesicle membrane / signaling receptor activity / amyloid-beta binding / basolateral plasma membrane / early endosome / receptor complex / lysosomal membrane / negative regulation of gene expression / focal adhesion / calcium ion binding / protein-containing complex binding / nucleolus / Golgi apparatus / RNA binding / membrane / plasma membrane / cytosol
Similarity search - Function
Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / 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 ...Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / 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 / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Prolow-density lipoprotein receptor-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DYNAMICS ANNEALING
AuthorsHuang, W. / Dolmer, K. / Gettins, P.G.W.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: NMR solution structure of complement-like repeat CR8 from the low density lipoprotein receptor-related protein.
Authors: Huang, W. / Dolmer, K. / Gettins, P.G.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / 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_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6962
Polymers4,6561
Non-polymers401
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 / 20LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein/peptide PROTEIN (LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN)


Mass: 4656.135 Da / Num. of mol.: 1 / Fragment: COMPLEMENT REPEAT 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER, PLACENTA / Plasmid: PGEX-2T / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07954
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY-HSQC
121TOCSY-HSQC
131(H)CCH-
NMR detailsText: FIRST. N-15 EDITED TOCSY-HSQC, NOESY-HSQC, HNHA C-13 EDITED HCCH-TOCSY, HCCH- NOESY, TRIPLE RESONANCE HNCA, HBHA(CO)NH

-
Sample preparation

Sample conditionsIonic strength: 0.05 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DMX600 / Manufacturer: Bruker / Model: DMX600 / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAstructure solution
RefinementMethod: DYNAMICS ANNEALING / Software ordinal: 1 / Details: ENERGY MINIMIZATION
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 20 / 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