[English] 日本語
Yorodumi
- PDB-2knx: Solution Structure of complement repeat CR17 from LRP-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2knx
TitleSolution Structure of complement repeat CR17 from LRP-1
ComponentsProlow-density lipoprotein receptor-related protein 1
KeywordsPROTEIN BINDING / LDLR / ligand binding module / ligand binding repeat / complement repeat
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / positive regulation of lysosomal protein catabolic process / aorta morphogenesis ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / positive regulation of lysosomal protein catabolic process / aorta morphogenesis / negative regulation of smooth muscle cell migration / regulation of cholesterol transport / clathrin heavy chain binding / amyloid-beta clearance by transcytosis / low-density lipoprotein particle receptor activity / regulation of extracellular matrix disassembly / amyloid-beta clearance by cellular catabolic process / scavenger receptor activity / 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 / retinoid metabolic process / lysosomal transport / microtubule organizing center / lipoprotein transport / enzyme-linked receptor protein signaling pathway / negative regulation of SMAD protein signal transduction / negative regulation of Wnt signaling pathway / amyloid-beta clearance / positive regulation of endocytosis / apolipoprotein binding / transport across blood-brain barrier / positive regulation of cholesterol efflux / Scavenging of heme from plasma / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / receptor-mediated endocytosis / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / lipid metabolic process / receptor internalization / cellular response to amyloid-beta / endocytic vesicle membrane / positive regulation of protein binding / 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 / Golgi apparatus / RNA binding / membrane / nucleus / plasma membrane
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 / Low-density lipoprotein-receptor YWTD domain ...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. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / 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 2. / EGF-like domain signature 1. / 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 / DGSA-distance geometry simulated annealing
Model detailsclosest to the average
AuthorsGuttman, M. / Komives, E.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the minimal interface between ApoE and LRP.
Authors: Guttman, M. / Prieto, J.H. / Handel, T.M. / Domaille, P.J. / Komives, E.A.
History
DepositionSep 7, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prolow-density lipoprotein receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1432
Polymers5,1031
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 93structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Prolow-density lipoprotein receptor-related protein 1 / LRP / Alpha-2-macroglobulin receptor / A2MR / Apolipoprotein E receptor / APOER / Low-density ...LRP / Alpha-2-macroglobulin receptor / A2MR / Apolipoprotein E receptor / APOER / Low-density lipoprotein receptor-related protein 1 85 kDa subunit / LRP-85 / Low-density lipoprotein receptor-related protein 1 515 kDa subunit / LRP-515 / Low-density lipoprotein receptor-related protein 1 intracellular domain / LRPICD


Mass: 5102.543 Da / Num. of mol.: 1 / Fragment: residues 2770-2817
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP1, A2MR, APR / Plasmid: pMMHB / 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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HCNH NOESY
11013D CBCANH
21112D 1H-15N HSQC heternuclear NOE
21212D 1H-15N HSQC T1 relaxation
21312D 1H-15N HSQC T2 relaxation

-
Sample preparation

DetailsContents: 150 mM sodium chloride, 20 mM [U-99% 2H] HEPES, 0.7 mM [U-99% 13C; U-99% 15N] protein, 5 mM CALCIUM ION, 3 mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMsodium chloride-11
20 mMHEPES-2[U-99% 2H]1
0.7 mMprotein-3[U-99% 13C; U-99% 15N]1
5 mMCALCIUM ION-41
3 mMsodium azide-51
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.15 7.45 ambient 307 K
20.15 7.45 ambient 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Azara2.7Boucherprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddarddata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 881 / NOE intraresidue total count: 169 / NOE long range total count: 200 / NOE medium range total count: 148 / NOE sequential total count: 152 / Hydrogen bond constraints total count: 6 / Protein phi angle constraints total count: 22 / Protein psi angle constraints total count: 22
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 93 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.5 Å / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.0555 Å / Distance rms dev error: 0.0031 Å

+
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://pdbjlvh1.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