[English] 日本語
Yorodumi
- PDB-2m0p: Solution structure of the tenth complement type repeat of human m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m0p
TitleSolution structure of the tenth complement type repeat of human megalin
ComponentsLow-density lipoprotein receptor-related protein 2
KeywordsLIPID BINDING PROTEIN / Complement type repeat / receptor / megalin / ldl receptor family / lrp2
Function / homology
Function and homology information


: / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of oligodendrocyte progenitor proliferation / folate import across plasma membrane / positive regulation of lysosomal protein catabolic process / metal ion transport / response to leptin / ventricular compact myocardium morphogenesis / protein transporter activity ...: / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of oligodendrocyte progenitor proliferation / folate import across plasma membrane / positive regulation of lysosomal protein catabolic process / metal ion transport / response to leptin / ventricular compact myocardium morphogenesis / protein transporter activity / Vitamin D (calciferol) metabolism / vitamin D metabolic process / clathrin-coated vesicle membrane / neuron projection arborization / coronary artery morphogenesis / outflow tract septum morphogenesis / membrane organization / insulin-like growth factor I binding / transcytosis / aorta development / retinoid metabolic process / ventricular septum development / positive regulation of neurogenesis / amyloid-beta clearance / vagina development / transport across blood-brain barrier / negative regulation of BMP signaling pathway / endocytic vesicle / Retinoid metabolism and transport / clathrin-coated pit / forebrain development / receptor-mediated endocytosis / kidney development / neural tube closure / endosome lumen / brush border membrane / sensory perception of sound / lipid metabolic process / cellular response to growth factor stimulus / SH3 domain binding / endocytosis / male gonad development / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / cell population proliferation / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / receptor complex / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / calcium ion binding / dendrite / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / extracellular exosome / plasma membrane
Similarity search - Function
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 ...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 / Legume lectin, beta chain, Mn/Ca-binding site / 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 / 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
Low-density lipoprotein receptor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDagil, R. / Kragelund, B.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type ...Title: Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin.
Authors: Dagil, R. / O'Shea, C. / Nykjar, A. / Bonvin, A.M. / Kragelund, B.B.
History
DepositionNov 1, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_nmr_spectrometer.model / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Low-density lipoprotein receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9142
Polymers5,8741
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Low-density lipoprotein receptor-related protein 2 / LRP-2 / Glycoprotein 330 / gp330 / Megalin


Mass: 5874.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP2 / Plasmid: pPICaC / Production host: Komagataella pastoris (fungus) / References: UniProt: P98164
#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
1312D 1H-1H TOCSY aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D C(CO)NH
1813D CBCA(CO)NH
1923D (H)CCH-TOCSY
11013D HN(CO)CA
11123D 1H-13C NOESY aliphatic
11222D 1H-13C NOESY aromatic
11313D H(CCO)NH
11413D 1H-15N NOESY
11513D 1H-15N TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] CR10, 100 mM sodium chloride, 50 mM calcium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 13C; U-100% 15N] CR10, 50 mM calcium chloride, 100 mM sodium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMCR10-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
50 mMcalcium chloride-31
50 mMTRIS-41
0.1 mMDSS-51
0.1 %sodium azide-61
0.6 mMCR10-7[U-100% 13C; U-100% 15N]2
50 mMcalcium chloride-82
100 mMsodium chloride-92
50 mMTRIS-102
0.1 mMDSS-112
0.1 %sodium azide-122
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002
Bruker AvanceBrukerAVANCE8003

-
Processing

NMR software
NameVersionDeveloperClassification
Analysis2.2CCPNchemical shift assignment
Analysis2.2CCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 555 / NOE intraresidue total count: 273 / NOE long range total count: 101 / NOE medium range total count: 87 / NOE sequential total count: 94 / Disulfide bond constraints total count: 3 / Hydrogen bond constraints total count: 15 / Protein phi angle constraints total count: 21 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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://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