[English] 日本語
Yorodumi
- PDB-1hj7: NMR study of a pair of LDL receptor Ca2+ binding epidermal growth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hj7
TitleNMR study of a pair of LDL receptor Ca2+ binding epidermal growth factor-like domains, 20 structures
ComponentsLDL RECEPTOR
KeywordsCELL-SURFACE RECEPTOR / CALCIUM-BINDING / EGF-LIKE DOMAIN / MODULE / APO-E / APO-B / LDL / VLDL
Function / homology
Function and homology information


receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance ...receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / positive regulation of triglyceride biosynthetic process / clathrin heavy chain binding / negative regulation of receptor recycling / intestinal cholesterol absorption / low-density lipoprotein particle receptor activity / Chylomicron clearance / amyloid-beta clearance by cellular catabolic process / low-density lipoprotein particle binding / response to caloric restriction / LDL clearance / high-density lipoprotein particle clearance / regulation of protein metabolic process / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / endolysosome membrane / cellular response to fatty acid / negative regulation of amyloid fibril formation / negative regulation of low-density lipoprotein particle clearance / regulation of cholesterol metabolic process / artery morphogenesis / negative regulation of protein metabolic process / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / retinoid metabolic process / cholesterol metabolic process / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / endocytosis / positive regulation of inflammatory response / apical part of cell / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / virus receptor activity / protease binding / basolateral plasma membrane / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome membrane / negative regulation of gene expression / external side of plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / positive regulation of gene expression / cell surface / Golgi apparatus / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site ...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 / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / 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 / Laminin / Laminin / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaha, S. / Handford, P.A. / Campbell, I.D. / Downing, A.K.
Citation
Journal: Structure / Year: 2001
Title: Solution Structure of the Ldl Receptor Egf-Ab Pair: A Paradigm for the Assembly of Tandem Calcium Binding Egf Domains
Authors: Saha, S. / Boyd, J. / Werner, J.M. / Knott, V. / Handford, P.A. / Campbell, I.D. / Downing, A.K.
#1: Journal: Methods Mol.Biol. / Year: 2002
Title: The Use of Dipolar Couplings for the Structure Refinement of a Pair of Calcium-Binding Egf Domains.
Authors: Boyd, J. / Campbell, I.D. / Downing, A.K.
#2: Journal: Biochemistry / Year: 2001
Title: The First Epidermal Growth Factor-Like Domain of the Low-Density Lipoprotein Receptor Contains a Noncanonical Calcium Binding Site
Authors: Malby, S. / Pickering, R. / Saha, S. / Smallridge, R.S. / Linse, S. / Downing, A.K.
History
DepositionJan 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Feb 14, 2018Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_mr / _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
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LDL RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9113
Polymers8,8311
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)20 / 280NO NOE, 3JHN OR 1JHN CONSTRAINTS VIOLATED BY > 0.5 A, 5 DEGREES OR 2 HERTZ
RepresentativeModel #1

-
Components

#1: Protein LDL RECEPTOR


Mass: 8830.804 Da / Num. of mol.: 1
Fragment: CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAIN PAIR, RESIDUES 293-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: TRANSMEMBRANE / Gene: LDLR / Plasmid: PQE30 (QIAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01130
#2: 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
1111H-NOESY
121COSY
131TOCSY
1411H-15N HSQC
151HMQC-J
161HSQC-NOESY
171HSQC-TOCSY
NMR detailsText: NOE DISTANCE CONSTRAINTS WERE DERIVED FROM CROSS PEAK INTENSITIES MEASURED IN 1H-HOMONUCLEAR AND 1H-15N HETERONUCLEAR NMR SPECTRA. COUPLING CONSTANTS USED TO DERIVE TORSION ANGLE CONSTRAINTS ...Text: NOE DISTANCE CONSTRAINTS WERE DERIVED FROM CROSS PEAK INTENSITIES MEASURED IN 1H-HOMONUCLEAR AND 1H-15N HETERONUCLEAR NMR SPECTRA. COUPLING CONSTANTS USED TO DERIVE TORSION ANGLE CONSTRAINTS WERE MEASURED IN A 1H-15N HMQC-J SPECTRUM. SEE REFERENCE 1 FOR DETAILS OF 1JHN CONSTRAINT IMPLEMENTATION.

-
Sample preparation

DetailsContents: SEE REFERENCES
Sample conditionsIonic strength: SEE REFERENCES / pH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built6001
GE OMEGAGEOMEGA7502

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGER STRUCTURAL STATISTICS: FROM EXPERIMENTAL DISTANCE CONSTRAINTS (A) RMS SIGMA DEVIATIONS FROM EXP. RESTRAINTS DEVIATIONS FROM IDEAL GEOMETRYrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN REFERENCE 1.
NMR ensembleConformer selection criteria: NO NOE, 3JHN OR 1JHN CONSTRAINTS VIOLATED BY > 0.5 A, 5 DEGREES OR 2 HERTZ
Conformers calculated total number: 280 / 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